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PDBsum entry 4dm9

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Hydrolase, ligase/inhibitor PDB id
4dm9
Jmol
Contents
Protein chain
223 a.a.
Ligands
PHQ-VAL-ALA-GME-
CF0
×2
Waters ×42
HEADER    HYDROLASE, LIGASE/INHIBITOR             07-FEB-12   4DM9
TITLE     THE CRYSTAL STRUCTURE OF UBIQUITIN CARBOXY-TERMINAL HYDROLASE L1
TITLE    2 (UCHL1) BOUND TO A TRIPEPTIDE FLUOROMETHYL KETONE Z-VAE(OME)-FMK
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L1;
COMPND   3 CHAIN: A, B;
COMPND   4 SYNONYM: UCH-L1, NEURON CYTOPLASMIC PROTEIN 9.5, PGP 9.5, PGP9.5,
COMPND   5 UBIQUITIN THIOESTERASE L1;
COMPND   6 EC: 3.4.19.12, 6.-.-.-;
COMPND   7 ENGINEERED: YES;
COMPND   8 MOL_ID: 2;
COMPND   9 MOLECULE: TRIPEPTIDE FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK;
COMPND  10 CHAIN: X, Y;
COMPND  11 ENGINEERED: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: UCHL1;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: ROSETTA;
SOURCE   9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE  10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P1;
SOURCE  11 MOL_ID: 2;
SOURCE  12 SYNTHETIC: YES
KEYWDS    UBIQUITIN HYDROLASE, LIGASE, HYDROLASE, LIGASE-INHIBITOR COMPLEX
EXPDTA    X-RAY DIFFRACTION
AUTHOR    C.W.DAVIES,J.CHANEY,G.KORBEL,D.RINGE,G.A.PETSKO,H.PLOEGH,C.DAS
REVDAT   2   13-JUN-12 4DM9    1       JRNL
REVDAT   1   23-MAY-12 4DM9    0
JRNL        AUTH   C.W.DAVIES,J.CHANEY,G.KORBEL,D.RINGE,G.A.PETSKO,H.PLOEGH,
JRNL        AUTH 2 C.DAS
JRNL        TITL   THE CO-CRYSTAL STRUCTURE OF UBIQUITIN CARBOXY-TERMINAL
JRNL        TITL 2 HYDROLASE L1 (UCHL1) WITH A TRIPEPTIDE FLUOROMETHYL KETONE
JRNL        TITL 3 (Z-VAE(OME)-FMK).
JRNL        REF    BIOORG.MED.CHEM.LETT.         V.  22  3900 2012
JRNL        REFN                   ISSN 0960-894X
JRNL        PMID   22617491
JRNL        DOI    10.1016/J.BMCL.2012.04.124
REMARK   2
REMARK   2 RESOLUTION.    2.35 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.7.3_928)
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-
REMARK   3               : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO,
REMARK   3               : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL
REMARK   3               : MORIARTY,REETAL PAI,RANDY READ,JANE
REMARK   3               : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM
REMARK   3               : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH,
REMARK   3               : LAURENT STORONI,TOM TERWILLIGER,PETER
REMARK   3               : ZWART
REMARK   3
REMARK   3    REFINEMENT TARGET : ML
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.35
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 34.87
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.340
REMARK   3   COMPLETENESS FOR RANGE        (%) : 97.9
REMARK   3   NUMBER OF REFLECTIONS             : 20267
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.200
REMARK   3   R VALUE            (WORKING SET) : 0.197
REMARK   3   FREE R VALUE                     : 0.250
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 5.120
REMARK   3   FREE R VALUE TEST SET COUNT      : 1037
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK   3   BIN  RESOLUTION RANGE  COMPL.    NWORK NFREE   RWORK  RFREE
REMARK   3     1 34.8766 -  4.4932    0.99     2978   138  0.1788 0.2368
REMARK   3     2  4.4932 -  3.5675    1.00     2842   132  0.1517 0.1803
REMARK   3     3  3.5675 -  3.1169    1.00     2777   168  0.2139 0.2458
REMARK   3     4  3.1169 -  2.8321    1.00     2753   162  0.2403 0.3503
REMARK   3     5  2.8321 -  2.6291    1.00     2747   165  0.2586 0.3077
REMARK   3     6  2.6291 -  2.4742    0.98     2696   138  0.2801 0.3371
REMARK   3     7  2.4742 -  2.3503    0.89     2437   134  0.3369 0.3832
REMARK   3
REMARK   3  BULK SOLVENT MODELLING.
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL
REMARK   3   SOLVENT RADIUS     : 1.10
REMARK   3   SHRINKAGE RADIUS   : 0.86
REMARK   3   K_SOL              : 0.36
REMARK   3   B_SOL              : 61.66
REMARK   3
REMARK   3  ERROR ESTIMATES.
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.380
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.820
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : NULL
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : 8.91500
REMARK   3    B22 (A**2) : 8.91500
REMARK   3    B33 (A**2) : -17.83010
REMARK   3    B12 (A**2) : 0.00000
REMARK   3    B13 (A**2) : -0.00000
REMARK   3    B23 (A**2) : 0.00000
REMARK   3
REMARK   3  TWINNING INFORMATION.
REMARK   3   FRACTION: NULL
REMARK   3   OPERATOR: NULL
REMARK   3
REMARK   3  DEVIATIONS FROM IDEAL VALUES.
REMARK   3                 RMSD          COUNT
REMARK   3   BOND      :  0.005           3611
REMARK   3   ANGLE     :  1.048           4856
REMARK   3   CHIRALITY :  0.088            530
REMARK   3   PLANARITY :  0.004            643
REMARK   3   DIHEDRAL  : 16.536           1361
REMARK   3
REMARK   3  TLS DETAILS
REMARK   3   NUMBER OF TLS GROUPS  : 11
REMARK   3   TLS GROUP : 1
REMARK   3    SELECTION: chain 'A' and (resseq 1:136)
REMARK   3    ORIGIN FOR THE GROUP (A):  36.1751  16.6399  14.5648
REMARK   3    T TENSOR
REMARK   3      T11:   0.2131 T22:   0.3525
REMARK   3      T33:   0.2420 T12:   0.0259
REMARK   3      T13:   0.0212 T23:   0.0842
REMARK   3    L TENSOR
REMARK   3      L11:   3.5907 L22:   5.6719
REMARK   3      L33:   3.8446 L12:  -0.4424
REMARK   3      L13:   0.8571 L23:   1.2130
REMARK   3    S TENSOR
REMARK   3      S11:  -0.1107 S12:  -0.0529 S13:  -0.0454
REMARK   3      S21:   0.0049 S22:   0.2731 S23:   0.2469
REMARK   3      S31:  -0.1560 S32:  -0.4633 S33:  -0.1397
REMARK   3   TLS GROUP : 2
REMARK   3    SELECTION: chain 'A' and (resseq 137:159)
REMARK   3    ORIGIN FOR THE GROUP (A):  47.4842  11.0402  23.1044
REMARK   3    T TENSOR
REMARK   3      T11:   0.5280 T22:   0.5180
REMARK   3      T33:   0.4218 T12:   0.1397
REMARK   3      T13:   0.0035 T23:   0.0267
REMARK   3    L TENSOR
REMARK   3      L11:   6.5915 L22:   1.5880
REMARK   3      L33:   9.0049 L12:   3.0473
REMARK   3      L13:  -6.6302 L23:  -3.5284
REMARK   3    S TENSOR
REMARK   3      S11:  -0.8111 S12:  -0.5419 S13:  -0.8537
REMARK   3      S21:  -0.0751 S22:   0.4172 S23:  -0.2754
REMARK   3      S31:   0.8797 S32:   0.6685 S33:   0.3267
REMARK   3   TLS GROUP : 3
REMARK   3    SELECTION: chain 'A' and (resseq 160:207)
REMARK   3    ORIGIN FOR THE GROUP (A):  33.0017  13.3556   3.4491
REMARK   3    T TENSOR
REMARK   3      T11:   0.3822 T22:   0.4472
REMARK   3      T33:   0.2619 T12:   0.0236
REMARK   3      T13:   0.0059 T23:   0.0383
REMARK   3    L TENSOR
REMARK   3      L11:   9.0015 L22:   8.0962
REMARK   3      L33:   7.4248 L12:  -1.4749
REMARK   3      L13:   5.4123 L23:  -2.0489
REMARK   3    S TENSOR
REMARK   3      S11:   0.0420 S12:   0.5642 S13:  -0.2451
REMARK   3      S21:  -0.7443 S22:   0.1874 S23:   0.4170
REMARK   3      S31:   0.1659 S32:  -0.2229 S33:  -0.2159
REMARK   3   TLS GROUP : 4
REMARK   3    SELECTION: chain 'A' and (resseq 208:223)
REMARK   3    ORIGIN FOR THE GROUP (A):  37.9014   3.8756   9.5624
REMARK   3    T TENSOR
REMARK   3      T11:   0.4350 T22:   0.5138
REMARK   3      T33:   0.5501 T12:  -0.1347
REMARK   3      T13:   0.0280 T23:   0.0346
REMARK   3    L TENSOR
REMARK   3      L11:   3.5202 L22:   8.1477
REMARK   3      L33:   4.8391 L12:  -5.2664
REMARK   3      L13:  -2.7472 L23:   4.9500
REMARK   3    S TENSOR
REMARK   3      S11:  -0.1862 S12:   0.2716 S13:   0.0443
REMARK   3      S21:  -0.1999 S22:   0.5389 S23:  -0.2362
REMARK   3      S31:   0.0577 S32:  -0.1825 S33:  -0.2875
REMARK   3   TLS GROUP : 5
REMARK   3    SELECTION: chain 'B' and (resseq 1:45)
REMARK   3    ORIGIN FOR THE GROUP (A):  54.8744  22.0824  44.8497
REMARK   3    T TENSOR
REMARK   3      T11:   0.4388 T22:   0.4528
REMARK   3      T33:   0.4536 T12:   0.0288
REMARK   3      T13:   0.1567 T23:   0.0054
REMARK   3    L TENSOR
REMARK   3      L11:   8.5730 L22:   6.4432
REMARK   3      L33:   7.8430 L12:  -0.9465
REMARK   3      L13:   2.9828 L23:   2.4268
REMARK   3    S TENSOR
REMARK   3      S11:   0.1544 S12:   0.2524 S13:   0.4820
REMARK   3      S21:  -0.4520 S22:   0.2010 S23:  -0.9860
REMARK   3      S31:  -0.8570 S32:   0.6289 S33:  -0.3269
REMARK   3   TLS GROUP : 6
REMARK   3    SELECTION: chain 'B' and (resseq 46:69)
REMARK   3    ORIGIN FOR THE GROUP (A):  44.4992  15.6694  61.6965
REMARK   3    T TENSOR
REMARK   3      T11:   0.4745 T22:   0.7314
REMARK   3      T33:   0.3201 T12:  -0.0556
REMARK   3      T13:   0.0121 T23:  -0.0587
REMARK   3    L TENSOR
REMARK   3      L11:   6.2654 L22:   8.2477
REMARK   3      L33:   4.1422 L12:   1.4365
REMARK   3      L13:  -0.4841 L23:  -0.2635
REMARK   3    S TENSOR
REMARK   3      S11:   0.2031 S12:  -0.5834 S13:  -0.4085
REMARK   3      S21:   1.0916 S22:  -0.1353 S23:   0.3504
REMARK   3      S31:  -0.0759 S32:  -1.3217 S33:  -0.0368
REMARK   3   TLS GROUP : 7
REMARK   3    SELECTION: chain 'B' and (resseq 70:136)
REMARK   3    ORIGIN FOR THE GROUP (A):  38.5733  26.7631  47.3766
REMARK   3    T TENSOR
REMARK   3      T11:   0.6049 T22:   0.6702
REMARK   3      T33:   0.4736 T12:   0.2618
REMARK   3      T13:  -0.0808 T23:  -0.0306
REMARK   3    L TENSOR
REMARK   3      L11:   5.0121 L22:   4.8274
REMARK   3      L33:   4.9971 L12:  -0.2953
REMARK   3      L13:  -0.7897 L23:   2.9375
REMARK   3    S TENSOR
REMARK   3      S11:   0.1364 S12:   0.2842 S13:   0.5280
REMARK   3      S21:  -0.5247 S22:  -0.1766 S23:   0.4168
REMARK   3      S31:  -1.2450 S32:  -1.0133 S33:   0.0176
REMARK   3   TLS GROUP : 8
REMARK   3    SELECTION: chain 'B' and (resseq 137:159)
REMARK   3    ORIGIN FOR THE GROUP (A):  46.7575  10.6179  40.4082
REMARK   3    T TENSOR
REMARK   3      T11:   0.6567 T22:   0.5312
REMARK   3      T33:   0.4898 T12:   0.2428
REMARK   3      T13:   0.1002 T23:  -0.0172
REMARK   3    L TENSOR
REMARK   3      L11:   5.1641 L22:   3.0443
REMARK   3      L33:   4.1343 L12:   3.9454
REMARK   3      L13:  -4.6078 L23:  -3.4781
REMARK   3    S TENSOR
REMARK   3      S11:  -0.0984 S12:   0.1664 S13:  -0.8112
REMARK   3      S21:  -0.6641 S22:  -0.5297 S23:  -0.0365
REMARK   3      S31:   0.3441 S32:   0.2036 S33:   0.5282
REMARK   3   TLS GROUP : 9
REMARK   3    SELECTION: chain 'B' and (resseq 160:189)
REMARK   3    ORIGIN FOR THE GROUP (A):  45.1064  25.5604  58.7128
REMARK   3    T TENSOR
REMARK   3      T11:   0.5241 T22:   0.4365
REMARK   3      T33:   0.3941 T12:   0.0657
REMARK   3      T13:  -0.0564 T23:  -0.0175
REMARK   3    L TENSOR
REMARK   3      L11:   8.1196 L22:   3.5896
REMARK   3      L33:   8.0553 L12:  -4.5360
REMARK   3      L13:  -0.6193 L23:   2.4615
REMARK   3    S TENSOR
REMARK   3      S11:  -0.0316 S12:  -0.1922 S13:   0.7677
REMARK   3      S21:   0.6923 S22:  -0.1819 S23:   0.0167
REMARK   3      S31:  -0.7578 S32:  -0.5968 S33:   0.1190
REMARK   3   TLS GROUP : 10
REMARK   3    SELECTION: chain 'B' and (resseq 190:207)
REMARK   3    ORIGIN FOR THE GROUP (A):  55.2659  24.7432  62.7919
REMARK   3    T TENSOR
REMARK   3      T11:   0.5265 T22:   0.6773
REMARK   3      T33:   0.6273 T12:   0.0300
REMARK   3      T13:  -0.0594 T23:  -0.1117
REMARK   3    L TENSOR
REMARK   3      L11:   3.8676 L22:   2.9590
REMARK   3      L33:   7.4628 L12:   2.3223
REMARK   3      L13:   1.6934 L23:  -0.7324
REMARK   3    S TENSOR
REMARK   3      S11:   0.3846 S12:  -0.9621 S13:   0.3042
REMARK   3      S21:   1.6720 S22:   0.2097 S23:  -0.2050
REMARK   3      S31:   0.1403 S32:  -0.0337 S33:  -0.4778
REMARK   3   TLS GROUP : 11
REMARK   3    SELECTION: chain 'B' and (resseq 208:223)
REMARK   3    ORIGIN FOR THE GROUP (A):  56.6024  17.7255  53.7477
REMARK   3    T TENSOR
REMARK   3      T11:   0.3839 T22:   0.5043
REMARK   3      T33:   0.4467 T12:  -0.0803
REMARK   3      T13:  -0.0738 T23:  -0.0300
REMARK   3    L TENSOR
REMARK   3      L11:   9.5371 L22:   4.1077
REMARK   3      L33:   9.0101 L12:  -5.7101
REMARK   3      L13:   3.9145 L23:  -1.0637
REMARK   3    S TENSOR
REMARK   3      S11:   0.0020 S12:  -0.5052 S13:  -0.0865
REMARK   3      S21:   0.5219 S22:   0.3936 S23:  -0.5478
REMARK   3      S31:  -0.6031 S32:   0.3883 S33:  -0.3503
REMARK   3
REMARK   3  NCS DETAILS
REMARK   3   NUMBER OF NCS GROUPS : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 4DM9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-12.
REMARK 100 THE RCSB ID CODE IS RCSB070506.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 06-FEB-06
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 7.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : Y
REMARK 200  RADIATION SOURCE               : APS
REMARK 200  BEAMLINE                       : 23-ID-D
REMARK 200  X-RAY GENERATOR MODEL          : NULL
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0
REMARK 200  MONOCHROMATOR                  : SI 111
REMARK 200  OPTICS                         : MIRRORS
REMARK 200
REMARK 200  DETECTOR TYPE                  : CCD
REMARK 200  DETECTOR MANUFACTURER          : MARMOSAIC 300 MM CCD
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 20326
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.350
REMARK 200  RESOLUTION RANGE LOW       (A) : 50.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.100
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 98.1
REMARK 200  DATA REDUNDANCY                : 12.900
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.05100
REMARK 200   FOR THE DATA SET  : 48.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.43
REMARK 200  COMPLETENESS FOR SHELL     (%) : 89.6
REMARK 200  DATA REDUNDANCY IN SHELL       : 7.80
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.49900
REMARK 200   FOR SHELL         : 2.100
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: 2ETL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 46.79
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M AMMONIUM SULFATE, 0.1M HEPES, PH
REMARK 280  7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,-Y,Z
REMARK 290       3555   -Y+1/2,X+1/2,Z
REMARK 290       4555   Y+1/2,-X+1/2,Z
REMARK 290       5555   -X+1/2,Y+1/2,-Z
REMARK 290       6555   X+1/2,-Y+1/2,-Z
REMARK 290       7555   Y,X,-Z
REMARK 290       8555   -Y,-X,-Z
REMARK 290
REMARK 290     WHERE NNN -> OPERATOR NUMBER
REMARK 290           MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       55.00550
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       55.00550
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       55.00550
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       55.00550
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        0.00000
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       55.00550
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       55.00550
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       55.00550
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       55.00550
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, X
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, Y
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000
REMARK 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375      HOH A 308  LIES ON A SPECIAL POSITION.
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465   M RES C SSSEQI
REMARK 465     GLY A    -4
REMARK 465     PRO A    -3
REMARK 465     LEU A    -2
REMARK 465     GLY A    -1
REMARK 465     SER A     0
REMARK 465     GLY B    -4
REMARK 465     PRO B    -3
REMARK 465     LEU B    -2
REMARK 465     GLY B    -1
REMARK 465     SER B     0
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500  M RES CSSEQI        PSI       PHI
REMARK 500    LYS A  71       -3.02     69.40
REMARK 500    CYS A 152      120.24    107.76
REMARK 500    ASP A 155      -69.25     46.72
REMARK 500    CYS B 152      121.72    110.21
REMARK 500    VAL B 154       -4.06     81.65
REMARK 500    LYS B 157       33.48    -63.01
REMARK 500    ALA B 222      118.67    -37.96
REMARK 500    ALA Y   3      -60.99     54.69
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500  M RES CSSEQI    IMPROPER   EXPECTED   FOUND DETAILS
REMARK 500    CYS A 152        18.4      L          L   OUTSIDE RANGE
REMARK 500    CYS B 152        19.0      L          L   OUTSIDE RANGE
REMARK 500    VAL Y   2        22.2      L          L   OUTSIDE RANGE
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN X OF TRIPEPTIDE
REMARK 800  FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN Y OF TRIPEPTIDE
REMARK 800  FLUOROMETHYL KETONE INHIBITOR Z-VAE(OME)-FMK
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2ETL   RELATED DB: PDB
REMARK 900 THE SAME PROTEIN WITHOUT FLUOROMETHYL KETONE INHBITOR
DBREF  4DM9 A    1   223  UNP    P09936   UCHL1_HUMAN      1    223
DBREF  4DM9 B    1   223  UNP    P09936   UCHL1_HUMAN      1    223
DBREF  4DM9 X    1     5  PDB    4DM9     4DM9             1      5
DBREF  4DM9 Y    1     5  PDB    4DM9     4DM9             1      5
SEQADV 4DM9 GLY A   -4  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 PRO A   -3  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 LEU A   -2  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 GLY A   -1  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 SER A    0  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 GLY B   -4  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 PRO B   -3  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 LEU B   -2  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 GLY B   -1  UNP  P09936              EXPRESSION TAG
SEQADV 4DM9 SER B    0  UNP  P09936              EXPRESSION TAG
SEQRES   1 A  228  GLY PRO LEU GLY SER MET GLN LEU LYS PRO MET GLU ILE
SEQRES   2 A  228  ASN PRO GLU MET LEU ASN LYS VAL LEU SER ARG LEU GLY
SEQRES   3 A  228  VAL ALA GLY GLN TRP ARG PHE VAL ASP VAL LEU GLY LEU
SEQRES   4 A  228  GLU GLU GLU SER LEU GLY SER VAL PRO ALA PRO ALA CYS
SEQRES   5 A  228  ALA LEU LEU LEU LEU PHE PRO LEU THR ALA GLN HIS GLU
SEQRES   6 A  228  ASN PHE ARG LYS LYS GLN ILE GLU GLU LEU LYS GLY GLN
SEQRES   7 A  228  GLU VAL SER PRO LYS VAL TYR PHE MET LYS GLN THR ILE
SEQRES   8 A  228  GLY ASN SER CYS GLY THR ILE GLY LEU ILE HIS ALA VAL
SEQRES   9 A  228  ALA ASN ASN GLN ASP LYS LEU GLY PHE GLU ASP GLY SER
SEQRES  10 A  228  VAL LEU LYS GLN PHE LEU SER GLU THR GLU LYS MET SER
SEQRES  11 A  228  PRO GLU ASP ARG ALA LYS CYS PHE GLU LYS ASN GLU ALA
SEQRES  12 A  228  ILE GLN ALA ALA HIS ASP ALA VAL ALA GLN GLU GLY GLN
SEQRES  13 A  228  CYS ARG VAL ASP ASP LYS VAL ASN PHE HIS PHE ILE LEU
SEQRES  14 A  228  PHE ASN ASN VAL ASP GLY HIS LEU TYR GLU LEU ASP GLY
SEQRES  15 A  228  ARG MET PRO PHE PRO VAL ASN HIS GLY ALA SER SER GLU
SEQRES  16 A  228  ASP THR LEU LEU LYS ASP ALA ALA LYS VAL CYS ARG GLU
SEQRES  17 A  228  PHE THR GLU ARG GLU GLN GLY GLU VAL ARG PHE SER ALA
SEQRES  18 A  228  VAL ALA LEU CYS LYS ALA ALA
SEQRES   1 B  228  GLY PRO LEU GLY SER MET GLN LEU LYS PRO MET GLU ILE
SEQRES   2 B  228  ASN PRO GLU MET LEU ASN LYS VAL LEU SER ARG LEU GLY
SEQRES   3 B  228  VAL ALA GLY GLN TRP ARG PHE VAL ASP VAL LEU GLY LEU
SEQRES   4 B  228  GLU GLU GLU SER LEU GLY SER VAL PRO ALA PRO ALA CYS
SEQRES   5 B  228  ALA LEU LEU LEU LEU PHE PRO LEU THR ALA GLN HIS GLU
SEQRES   6 B  228  ASN PHE ARG LYS LYS GLN ILE GLU GLU LEU LYS GLY GLN
SEQRES   7 B  228  GLU VAL SER PRO LYS VAL TYR PHE MET LYS GLN THR ILE
SEQRES   8 B  228  GLY ASN SER CYS GLY THR ILE GLY LEU ILE HIS ALA VAL
SEQRES   9 B  228  ALA ASN ASN GLN ASP LYS LEU GLY PHE GLU ASP GLY SER
SEQRES  10 B  228  VAL LEU LYS GLN PHE LEU SER GLU THR GLU LYS MET SER
SEQRES  11 B  228  PRO GLU ASP ARG ALA LYS CYS PHE GLU LYS ASN GLU ALA
SEQRES  12 B  228  ILE GLN ALA ALA HIS ASP ALA VAL ALA GLN GLU GLY GLN
SEQRES  13 B  228  CYS ARG VAL ASP ASP LYS VAL ASN PHE HIS PHE ILE LEU
SEQRES  14 B  228  PHE ASN ASN VAL ASP GLY HIS LEU TYR GLU LEU ASP GLY
SEQRES  15 B  228  ARG MET PRO PHE PRO VAL ASN HIS GLY ALA SER SER GLU
SEQRES  16 B  228  ASP THR LEU LEU LYS ASP ALA ALA LYS VAL CYS ARG GLU
SEQRES  17 B  228  PHE THR GLU ARG GLU GLN GLY GLU VAL ARG PHE SER ALA
SEQRES  18 B  228  VAL ALA LEU CYS LYS ALA ALA
SEQRES   1 X    5  PHQ VAL ALA GME CF0
SEQRES   1 Y    5  PHQ VAL ALA GME CF0
MODRES 4DM9 GME X    4  GLU  5-O-METHYL-GLUTAMIC ACID
MODRES 4DM9 GME Y    4  GLU  5-O-METHYL-GLUTAMIC ACID
HET    PHQ  X   1      10
HET    GME  X   4      10
HET    CF0  X   5       1
HET    PHQ  Y   1      10
HET    GME  Y   4      10
HET    CF0  Y   5       1
HETNAM     PHQ BENZYL CHLOROCARBONATE
HETNAM     GME 5-O-METHYL-GLUTAMIC ACID
HETNAM     CF0 FLUOROMETHANE
HETSYN     GME (2S)-2-AMINO-5-METHOXY-5-OXOPENTANOIC ACID
HETSYN     CF0 FLUORO METHYL GROUP
FORMUL   3  PHQ    2(C8 H7 CL O2)
FORMUL   3  GME    2(C6 H11 N O4)
FORMUL   3  CF0    2(C H3 F)
FORMUL   5  HOH   *42(H2 O)
HELIX    1   1 ASN A    9  LEU A   20  1                                  12
HELIX    2   2 GLU A   35  SER A   41  1                                   7
HELIX    3   3 THR A   56  LYS A   71  1                                  16
HELIX    4   4 SER A   89  ASN A  101  1                                  13
HELIX    5   5 SER A  112  THR A  121  1                                  10
HELIX    6   6 SER A  125  LYS A  135  1                                  11
HELIX    7   7 ASN A  136  GLN A  148  1                                  13
HELIX    8   8 SER A  189  ASP A  191  5                                   3
HELIX    9   9 THR A  192  GLU A  208  1                                  17
HELIX   10  10 ASN B    9  LEU B   20  1                                  12
HELIX   11  11 GLU B   35  SER B   41  1                                   7
HELIX   12  12 THR B   56  LEU B   70  1                                  15
HELIX   13  13 SER B   89  ASN B  101  1                                  13
HELIX   14  14 SER B  112  THR B  121  1                                  10
HELIX   15  15 SER B  125  LYS B  135  1                                  11
HELIX   16  16 ASN B  136  GLN B  148  1                                  13
HELIX   17  17 SER B  189  ASP B  191  5                                   3
HELIX   18  18 THR B  192  GLU B  208  1                                  17
SHEET    1   A 6 TRP A  26  VAL A  31  0
SHEET    2   A 6 SER A 215  LYS A 221 -1  O  CYS A 220   N  ARG A  27
SHEET    3   A 6 ALA A  46  PRO A  54 -1  N  LEU A  52   O  SER A 215
SHEET    4   A 6 PHE A 160  VAL A 168 -1  O  ILE A 163   N  LEU A  51
SHEET    5   A 6 HIS A 171  LEU A 175 -1  O  TYR A 173   N  ASN A 166
SHEET    6   A 6 VAL A 183  ALA A 187 -1  O  HIS A 185   N  LEU A 172
SHEET    1   B 6 TRP B  26  VAL B  31  0
SHEET    2   B 6 SER B 215  LYS B 221 -1  O  CYS B 220   N  ARG B  27
SHEET    3   B 6 ALA B  46  PRO B  54 -1  N  LEU B  52   O  SER B 215
SHEET    4   B 6 PHE B 160  VAL B 168 -1  O  ILE B 163   N  LEU B  51
SHEET    5   B 6 HIS B 171  LEU B 175 -1  O  TYR B 173   N  ASN B 166
SHEET    6   B 6 VAL B 183  ALA B 187 -1  O  HIS B 185   N  LEU B 172
LINK         C1  PHQ X   1                 N   VAL X   2     1555   1555  1.43
LINK         C   ALA X   3                 N   GME X   4     1555   1555  1.33
LINK         C   GME X   4                 C1  CF0 X   5     1555   1555  1.54
LINK         C1  PHQ Y   1                 N   VAL Y   2     1555   1555  1.43
LINK         C   ALA Y   3                 N   GME Y   4     1555   1555  1.33
LINK         C   GME Y   4                 C1  CF0 Y   5     1555   1555  1.54
LINK         SG  CYS A  90                 C1  CF0 X   5     1555   1555  1.80
LINK         SG  CYS B  90                 C1  CF0 Y   5     1555   1555  1.80
CISPEP   1 ALA A   44    PRO A   45          0        -2.35
CISPEP   2 ALA B   44    PRO B   45          0        -2.39
SITE     1 AC1 18 MET A   6  VAL A  31  LEU A  32  GLY A  33
SITE     2 AC1 18 LEU A  34  GLN A  84  GLY A  87  ASN A  88
SITE     3 AC1 18 SER A  89  CYS A  90  ARG A 153  ASN A 159
SITE     4 AC1 18 PHE A 160  ARG A 178  PHE A 214  SER A 215
SITE     5 AC1 18 ALA A 216  HOH X 101
SITE     1 AC2 17 VAL B  31  LEU B  32  GLY B  33  LEU B  34
SITE     2 AC2 17 GLN B  84  GLY B  87  ASN B  88  SER B  89
SITE     3 AC2 17 CYS B  90  ARG B 153  LYS B 157  VAL B 158
SITE     4 AC2 17 ASN B 159  PHE B 160  ARG B 178  PHE B 214
SITE     5 AC2 17 HOH Y 101
CRYST1  110.011  110.011   78.745  90.00  90.00  90.00 P 4 21 2     16
ORIGX1      1.000000  0.000000  0.000000        0.00000
ORIGX2      0.000000  1.000000  0.000000        0.00000
ORIGX3      0.000000  0.000000  1.000000        0.00000
SCALE1      0.009090  0.000000  0.000000        0.00000
SCALE2      0.000000  0.009090  0.000000        0.00000
SCALE3      0.000000  0.000000  0.012699        0.00000
      
PROCHECK
Go to PROCHECK summary
 References