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PDBsum entry 3dc9

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Lyase PDB id
3dc9
Jmol
Contents
Protein chain
257 a.a.
Metals
_ZN
Waters ×188
HEADER    LYASE                                   03-JUN-08   3DC9
TITLE     USE OF CARBONIC ANHYDRASE II, IX ACTIVE-SITE MIMIC, FOR THE
TITLE    2 PURPOSE OF SCREENING INHIBITORS FOR POSSIBLE ANTI-CANCER
TITLE    3 PROPERTIES
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CARBONIC ANHYDRASE 2;
COMPND   3 CHAIN: A;
COMPND   4 SYNONYM: CARBONIC ANHYDRASE II, CARBONATE DEHYDRATASE II,
COMPND   5 CA-II, CARBONIC ANHYDRASE C, CAC;
COMPND   6 EC: 4.2.1.1;
COMPND   7 ENGINEERED: YES;
COMPND   8 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 GENE: CA2;
SOURCE   6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    CARBONIC ANHYDRASE II COMPLEX, CAIX MIMIC INHIBITORS,
KEYWDS   2 ACETYLATION, CYTOPLASM, DISEASE MUTATION, LYASE, METAL-
KEYWDS   3 BINDING, POLYMORPHISM, ZINC
EXPDTA    X-RAY DIFFRACTION
AUTHOR    C.GENIS,K.H.SIPPEL,N.CASE,L.GOVINDASAMY,M.AGBANDJE-MCKENNA,
AUTHOR   2 R.MCKENNA
REVDAT   2   07-JUL-09 3DC9    1       JRNL
REVDAT   1   03-MAR-09 3DC9    0
JRNL        AUTH   C.GENIS,K.H.SIPPEL,N.CASE,W.CAO,B.S.AVVARU,
JRNL        AUTH 2 L.J.TARTAGLIA,L.GOVINDASAMY,C.TU,
JRNL        AUTH 3 M.AGBANDJE-MCKENNA,D.N.SILVERMAN,C.J.ROSSER,
JRNL        AUTH 4 R.MCKENNA
JRNL        TITL   DESIGN OF A CARBONIC ANHYDRASE IX ACTIVE-SITE MIMIC
JRNL        TITL 2 TO SCREEN INHIBITORS FOR POSSIBLE ANTICANCER
JRNL        TITL 3 PROPERTIES
JRNL        REF    BIOCHEMISTRY                  V.  48  1322 2009
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   19170619
JRNL        DOI    10.1021/BI802035F
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    1.60 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : SHELXL-97
REMARK   3   AUTHORS     : G.M.SHELDRICK
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 19.03
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000
REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.9
REMARK   3   CROSS-VALIDATION METHOD           : FREE R
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.160
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.200
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 31389
REMARK   3
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : 0.151
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : 26789
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS      : 2082
REMARK   3   NUCLEIC ACID ATOMS : 0
REMARK   3   HETEROGEN ATOMS    : 1
REMARK   3   SOLVENT ATOMS      : 188
REMARK   3
REMARK   3  MODEL REFINEMENT.
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : 2202.00
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : 0.00
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : 5
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : 9087
REMARK   3   NUMBER OF RESTRAINTS                     : 8699
REMARK   3
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK   3   BOND LENGTHS                         (A) : 0.008
REMARK   3   ANGLE DISTANCES                      (A) : 0.026
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : 0.029
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : 0.047
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : 0.063
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : 0.010
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : 0.000
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : 0.078
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : 0.000
REMARK   3
REMARK   3  BULK SOLVENT MODELING.
REMARK   3   METHOD USED: NULL
REMARK   3
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER
REMARK   3   SPECIAL CASE: NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 3DC9 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-08.
REMARK 100 THE RCSB ID CODE IS RCSB047857.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : NULL
REMARK 200  TEMPERATURE           (KELVIN) : 100
REMARK 200  PH                             : 9.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU RU200
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.54178
REMARK 200  MONOCHROMATOR                  : GRAPHITE
REMARK 200  OPTICS                         : OSMIC MIRROR
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IV++
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 31389
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.600
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.9
REMARK 200  DATA REDUNDANCY                : 3.000
REMARK 200  R MERGE                    (I) : NULL
REMARK 200  R SYM                      (I) : 0.07400
REMARK 200   FOR THE DATA SET  : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.66
REMARK 200  COMPLETENESS FOR SHELL     (%) : 91.4
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL
REMARK 200  R MERGE FOR SHELL          (I) : NULL
REMARK 200  R SYM FOR SHELL            (I) : 0.27900
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO
REMARK 200 SOFTWARE USED: SHELX
REMARK 200 STARTING MODEL: PDB ENTRY 1MOO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 42.74
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M SODIUM CITRATE, 100MM TRIS-
REMARK 280  HCL, PH 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,Y+1/2,-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       20.87500
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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 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     MET A     1
REMARK 465     SER A     2
REMARK 465     HIS A     3
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    ASN A  11       17.37   -140.32
REMARK 500    ASN A 244       51.00    -94.64
REMARK 500    LYS A 252     -140.21     58.28
REMARK 500    ASN A 253       45.51    -80.49
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620  (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620  SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL
REMARK 620                              ZN A 262  ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A  94   NE2
REMARK 620 2 HIS A  96   NE2 108.2
REMARK 620 3 HIS A 119   ND1 111.4  98.0
REMARK 620 4 HOH A 316   O   106.2 115.8 117.0
REMARK 620 N                    1     2     3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 262
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3D8W   RELATED DB: PDB
REMARK 900 RELATED ID: 3D9Z   RELATED DB: PDB
REMARK 900 RELATED ID: 3DBU   RELATED DB: PDB
REMARK 900 RELATED ID: 3DC3   RELATED DB: PDB
REMARK 900 RELATED ID: 3DCC   RELATED DB: PDB
REMARK 900 RELATED ID: 3DAZ   RELATED DB: PDB
DBREF  3DC9 A    1   261  UNP    P00918   CAH2_HUMAN       1    260
SEQADV 3DC9 SER A   65  UNP  P00918    ALA    65 ENGINEERED
SEQADV 3DC9 GLN A   67  UNP  P00918    ASN    67 ENGINEERED
SEQRES   1 A  260  MET SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO
SEQRES   2 A  260  GLU HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU
SEQRES   3 A  260  ARG GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS
SEQRES   4 A  260  TYR ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP
SEQRES   5 A  260  GLN ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS SER
SEQRES   6 A  260  PHE GLN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL
SEQRES   7 A  260  LEU LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE
SEQRES   8 A  260  GLN PHE HIS PHE HIS TRP GLY SER LEU ASP GLY GLN GLY
SEQRES   9 A  260  SER GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU
SEQRES  10 A  260  LEU HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE
SEQRES  11 A  260  GLY LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU
SEQRES  12 A  260  GLY ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU
SEQRES  13 A  260  GLN LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS
SEQRES  14 A  260  GLY LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY
SEQRES  15 A  260  LEU LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY
SEQRES  16 A  260  SER LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP
SEQRES  17 A  260  ILE VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN
SEQRES  18 A  260  VAL LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY
SEQRES  19 A  260  GLU PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA
SEQRES  20 A  260  GLN PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS
HET     ZN  A 262       1
HETNAM      ZN ZINC ION
FORMUL   2   ZN    ZN 2+
FORMUL   3  HOH   *188(H2 O)
HELIX    1   1 GLY A   12  ASP A   19  5                                   8
HELIX    2   2 PHE A   20  GLY A   25  5                                   6
HELIX    3   3 LYS A  127  GLY A  129  5                                   3
HELIX    4   4 ASP A  130  VAL A  135  1                                   6
HELIX    5   5 LYS A  154  GLY A  156  5                                   3
HELIX    6   6 LEU A  157  LEU A  164  1                                   8
HELIX    7   7 ASP A  165  LYS A  168  5                                   4
HELIX    8   8 ASP A  180  LEU A  185  5                                   6
HELIX    9   9 SER A  219  ARG A  227  1                                   9
SHEET    1   A 2 ASP A  32  ILE A  33  0
SHEET    2   A 2 THR A 108  VAL A 109  1  O  THR A 108   N  ILE A  33
SHEET    1   B10 LYS A  39  TYR A  40  0
SHEET    2   B10 LYS A 257  ALA A 258  1  O  ALA A 258   N  LYS A  39
SHEET    3   B10 TYR A 191  GLY A 196 -1  N  THR A 193   O  LYS A 257
SHEET    4   B10 VAL A 207  LEU A 212 -1  O  VAL A 207   N  GLY A 196
SHEET    5   B10 LEU A 141  VAL A 150  1  N  GLY A 145   O  LEU A 212
SHEET    6   B10 ALA A 116  ASN A 124 -1  N  LEU A 118   O  ILE A 146
SHEET    7   B10 TYR A  88  TRP A  97 -1  N  HIS A  94   O  HIS A 119
SHEET    8   B10 PHE A  66  PHE A  70 -1  N  PHE A  70   O  ILE A  91
SHEET    9   B10 SER A  56  ASN A  61 -1  N  LEU A  57   O  GLU A  69
SHEET   10   B10 SER A 173  ASP A 175 -1  O  ALA A 174   N  ILE A  59
SHEET    1   C 6 LEU A  47  SER A  50  0
SHEET    2   C 6 VAL A  78  GLY A  81 -1  O  LYS A  80   N  SER A  48
SHEET    3   C 6 TYR A  88  TRP A  97 -1  O  TYR A  88   N  LEU A  79
SHEET    4   C 6 ALA A 116  ASN A 124 -1  O  HIS A 119   N  HIS A  94
SHEET    5   C 6 LEU A 141  VAL A 150 -1  O  ILE A 146   N  LEU A 118
SHEET    6   C 6 ILE A 216  VAL A 218  1  O  ILE A 216   N  PHE A 147
LINK         NE2 HIS A  94                ZN    ZN A 262     1555   1555  2.06
LINK         NE2 HIS A  96                ZN    ZN A 262     1555   1555  2.04
LINK         ND1 HIS A 119                ZN    ZN A 262     1555   1555  2.08
LINK        ZN    ZN A 262                 O   HOH A 316     1555   1555  1.91
CISPEP   1 SER A   29    PRO A   30          0         1.25
CISPEP   2 PRO A  201    PRO A  202          0         7.43
SITE     1 AC1  4 HIS A  94  HIS A  96  HIS A 119  HOH A 316
CRYST1   42.810   41.750   72.790  90.00 104.48  90.00 P 1 21 1      2
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      0.023358  0.000000  0.006032        0.00000
SCALE2      0.000000  0.023955  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014189        0.00000
      
PROCHECK
Go to PROCHECK summary
 References