HEADER TRANSFERASE 09-JUN-09 3HRF TITLE CRYSTAL STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH AN TITLE 2 ALLOSTERIC ACTIVATOR BOUND TO THE PIF-POCKET COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDK1 KINASE DOMAIN; COMPND 5 SYNONYM: HPDK1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 CELL_LINE: SF9; SOURCE 5 GENE: PDK1, PDPK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS AGC KINASE, PHOSPHORYLATION, ALLOSTERY, PDK1, PIF-POCKET, ALPHA-C KEYWDS 2 HELIX, ACTIVATION LOOP, ATP BINDING, ATP-BINDING, KINASE, MEMBRANE, KEYWDS 3 NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, SERINE/THREONINE-PROTEIN KINASE, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR V.HINDIE,P.M.ALZARI,R.M.BIONDI REVDAT 4 10-NOV-21 3HRF 1 REMARK SEQADV LINK REVDAT 3 13-NOV-13 3HRF 1 JRNL REVDAT 2 13-JUL-11 3HRF 1 VERSN REVDAT 1 15-SEP-09 3HRF 0 JRNL AUTH V.HINDIE,A.STROBA,H.ZHANG,L.A.LOPEZ-GARCIA,L.IDRISSOVA, JRNL AUTH 2 S.ZEUZEM,D.HIRSCHBERG,F.SCHAEFFER,T.J.JRGENSEN,M.ENGEL, JRNL AUTH 3 P.M.ALZARI,R.M.BIONDI JRNL TITL STRUCTURE AND ALLOSTERIC EFFECTS OF LOW-MOLECULAR-WEIGHT JRNL TITL 2 ACTIVATORS ON THE PROTEIN KINASE PDK1. JRNL REF NAT.CHEM.BIOL. V. 5 758 2009 JRNL REFN ISSN 1552-4450 JRNL PMID 19718043 JRNL DOI 10.1038/NCHEMBIO.208 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.STROBA,F.SCHAEFFER,V.HINDIE,L.A.LOPEZ-GARCIA,W.FROHNER, REMARK 1 AUTH 2 I.ADRIAN,R.W.HARTMANN,R.M.BIONDI,M.ENGEL REMARK 1 TITL 3,5-DIPHENYL PENT-2-ENOIC ACIDS AS ALLOSTERIC ACTIVATORS OF REMARK 1 TITL 2 THE PROTEIN KINASE PDK1: STRUCTURE-ACTIVITY RELATIONSHIPS REMARK 1 TITL 3 AND THERMODYNAMIC CHARACTERISATION OF BINDING AS A PARADIGM REMARK 1 TITL 4 FOR PIF-BINDING POCKET-TARGETING COMPOUNDS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 23490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.600 REMARK 3 FREE R VALUE TEST SET COUNT : 384 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1718 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.1790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 16.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.36000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : 0.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.45000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.132 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2391 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3243 ; 1.463 ; 2.008 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 290 ; 5.704 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;32.923 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 400 ;12.280 ;15.038 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;23.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 353 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1764 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1433 ; 0.690 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2310 ; 1.318 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 958 ; 2.400 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 931 ; 3.922 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 6 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 75 A 161 REMARK 3 RESIDUE RANGE : A 162 A 359 REMARK 3 RESIDUE RANGE : A 1373 A 1373 REMARK 3 RESIDUE RANGE : A 1374 A 1374 REMARK 3 RESIDUE RANGE : A 1375 A 1375 REMARK 3 RESIDUE RANGE : A 1376 A 1376 REMARK 3 ORIGIN FOR THE GROUP (A): 24.1470 -22.7530 -25.5250 REMARK 3 T TENSOR REMARK 3 T11: 0.0197 T22: 0.0332 REMARK 3 T33: 0.0099 T12: -0.0045 REMARK 3 T13: -0.0125 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.8871 L22: 0.4049 REMARK 3 L33: 0.9172 L12: 0.0695 REMARK 3 L13: -0.2984 L23: 0.1212 REMARK 3 S TENSOR REMARK 3 S11: 0.0209 S12: -0.0513 S13: 0.0170 REMARK 3 S21: 0.0316 S22: -0.0312 S23: -0.0130 REMARK 3 S31: -0.0303 S32: -0.0703 S33: 0.0102 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3HRF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053491. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23875 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3HRC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4M SODIUM CITRATE, 0.1M SODIUM HEPES REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 74.27500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.27500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.00000 REMARK 290 SMTRY3 4 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 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 498 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 49 REMARK 465 ALA A 50 REMARK 465 MET A 51 REMARK 465 ASP A 52 REMARK 465 GLY A 53 REMARK 465 THR A 54 REMARK 465 ALA A 55 REMARK 465 ALA A 56 REMARK 465 GLU A 57 REMARK 465 PRO A 58 REMARK 465 ARG A 59 REMARK 465 PRO A 60 REMARK 465 GLY A 61 REMARK 465 ALA A 62 REMARK 465 GLY A 63 REMARK 465 SER A 64 REMARK 465 LEU A 65 REMARK 465 GLN A 66 REMARK 465 HIS A 67 REMARK 465 ALA A 68 REMARK 465 GLN A 69 REMARK 465 PRO A 70 REMARK 465 PRO A 71 REMARK 465 PRO A 72 REMARK 465 GLN A 73 REMARK 465 PRO A 74 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 78 NE CZ NH1 NH2 REMARK 470 LYS A 83 CE NZ REMARK 470 ARG A 100 CZ NH1 NH2 REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 120 CD CE NZ REMARK 470 GLU A 153 CD OE1 OE2 REMARK 470 LYS A 173 CD CE NZ REMARK 470 GLU A 209 CD OE1 OE2 REMARK 470 GLU A 215 CD OE1 OE2 REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 ARG A 238 CD NE CZ NH1 NH2 REMARK 470 GLU A 256 CD OE1 OE2 REMARK 470 LYS A 257 CG CD CE NZ REMARK 470 LYS A 293 CE NZ REMARK 470 GLU A 298 OE1 OE2 REMARK 470 ASP A 300 CG OD1 OD2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 ASN A 349 OD1 ND2 REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 THR A 359 OG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 48 O HOH A 505 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 138 81.98 -150.67 REMARK 500 ASP A 151 -162.13 -123.60 REMARK 500 SER A 176 119.20 -169.45 REMARK 500 ARG A 204 -10.73 76.59 REMARK 500 ASP A 223 77.12 75.25 REMARK 500 LYS A 304 7.92 81.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EPE A 1375 REMARK 610 EPE A 1376 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1373 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE P47 A 1374 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1375 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 1376 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3HRC RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 GLY49 AND ALA50 ARE FROM TEV CLEAVAGE DBREF 3HRF A 51 359 UNP O15530 PDPK1_HUMAN 51 359 SEQADV 3HRF GLY A 49 UNP O15530 SEE REMARK 999 SEQADV 3HRF ALA A 50 UNP O15530 SEE REMARK 999 SEQADV 3HRF GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 3HRF ALA A 292 UNP O15530 GLN 292 ENGINEERED MUTATION SEQRES 1 A 311 GLY ALA MET ASP GLY THR ALA ALA GLU PRO ARG PRO GLY SEQRES 2 A 311 ALA GLY SER LEU GLN HIS ALA GLN PRO PRO PRO GLN PRO SEQRES 3 A 311 ARG LYS LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE SEQRES 4 A 311 LEU GLY GLU GLY SER PHE SER THR VAL VAL LEU ALA ARG SEQRES 5 A 311 GLU LEU ALA THR SER ARG GLU TYR ALA ILE LYS ILE LEU SEQRES 6 A 311 GLU LYS ARG HIS ILE ILE LYS GLU ASN LYS VAL PRO TYR SEQRES 7 A 311 VAL THR ARG GLU ARG ASP VAL MET SER ARG LEU ASP HIS SEQRES 8 A 311 PRO PHE PHE VAL LYS LEU TYR PHE THR PHE GLN ASP ASP SEQRES 9 A 311 GLU LYS LEU TYR PHE GLY LEU SER TYR ALA LYS ASN GLY SEQRES 10 A 311 GLU LEU LEU LYS TYR ILE ARG LYS ILE GLY SER PHE ASP SEQRES 11 A 311 GLU THR CYS THR ARG PHE TYR THR ALA GLU ILE VAL SER SEQRES 12 A 311 ALA LEU GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG SEQRES 13 A 311 ASP LEU LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP MET SEQRES 14 A 311 HIS ILE GLN ILE THR ASP PHE GLY THR ALA LYS VAL LEU SEQRES 15 A 311 SER PRO GLU SER LYS GLN ALA ARG ALA ASN SEP PHE VAL SEQRES 16 A 311 GLY THR ALA GLN TYR VAL SER PRO GLU LEU LEU THR GLU SEQRES 17 A 311 LYS SER ALA CYS LYS SER SER ASP LEU TRP ALA LEU GLY SEQRES 18 A 311 CYS ILE ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE SEQRES 19 A 311 ARG ALA GLY ASN GLU GLY LEU ILE PHE ALA LYS ILE ILE SEQRES 20 A 311 LYS LEU GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS SEQRES 21 A 311 ALA ARG ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA SEQRES 22 A 311 THR LYS ARG LEU GLY CYS GLU GLU MET GLU GLY TYR GLY SEQRES 23 A 311 PRO LEU LYS ALA HIS PRO PHE PHE GLU SER VAL THR TRP SEQRES 24 A 311 GLU ASN LEU HIS GLN GLN THR PRO PRO LYS LEU THR MODRES 3HRF SEP A 241 SER PHOSPHOSERINE HET SEP A 241 10 HET ATP A1373 31 HET P47 A1374 20 HET EPE A1375 11 HET EPE A1376 11 HETNAM SEP PHOSPHOSERINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM P47 (2Z)-5-(4-CHLOROPHENYL)-3-PHENYLPENT-2-ENOIC ACID HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN SEP PHOSPHONOSERINE HETSYN EPE HEPES FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 P47 C17 H15 CL O2 FORMUL 4 EPE 2(C8 H18 N2 O4 S) FORMUL 6 HOH *189(H2 O) HELIX 1 1 ARG A 78 GLU A 80 5 3 HELIX 2 2 LYS A 115 GLU A 121 1 7 HELIX 3 3 LYS A 123 SER A 135 1 13 HELIX 4 4 LEU A 167 GLY A 175 1 9 HELIX 5 5 ASP A 178 LYS A 199 1 22 HELIX 6 6 LYS A 207 GLU A 209 5 3 HELIX 7 7 THR A 245 VAL A 249 5 5 HELIX 8 8 SER A 250 GLU A 256 1 7 HELIX 9 9 CYS A 260 GLY A 278 1 19 HELIX 10 10 ASN A 286 LEU A 297 1 12 HELIX 11 11 PHE A 306 LEU A 317 1 12 HELIX 12 12 ASP A 320 ARG A 324 5 5 HELIX 13 13 CYS A 327 GLU A 331 5 5 HELIX 14 14 GLY A 332 ALA A 338 1 7 HELIX 15 15 HIS A 339 GLU A 343 5 5 HELIX 16 16 THR A 346 GLN A 353 5 8 SHEET 1 A 5 PHE A 82 GLU A 90 0 SHEET 2 A 5 THR A 95 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 A 5 GLU A 107 GLU A 114 -1 O ILE A 110 N VAL A 97 SHEET 4 A 5 LYS A 154 LEU A 159 -1 O LEU A 159 N ALA A 109 SHEET 5 A 5 LEU A 145 GLN A 150 -1 N PHE A 147 O GLY A 158 SHEET 1 B 3 GLY A 165 GLU A 166 0 SHEET 2 B 3 ILE A 211 LEU A 213 -1 O LEU A 213 N GLY A 165 SHEET 3 B 3 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 SHEET 1 C 2 ILE A 201 ILE A 202 0 SHEET 2 C 2 LYS A 228 VAL A 229 -1 O LYS A 228 N ILE A 202 LINK C ASN A 240 N SEP A 241 1555 1555 1.33 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 SITE 1 AC1 21 HOH A 16 GLY A 89 GLY A 91 SER A 92 SITE 2 AC1 21 SER A 94 VAL A 96 ALA A 109 LYS A 111 SITE 3 AC1 21 SER A 160 ALA A 162 GLU A 166 LEU A 212 SITE 4 AC1 21 ASP A 223 HOH A 363 HOH A 395 HOH A 403 SITE 5 AC1 21 HOH A 441 HOH A 467 HOH A 471 HOH A 474 SITE 6 AC1 21 HOH A 506 SITE 1 AC2 11 LYS A 76 ILE A 119 VAL A 127 ARG A 131 SITE 2 AC2 11 THR A 148 PHE A 149 GLN A 150 LEU A 155 SITE 3 AC2 11 TYR A 156 PHE A 157 HOH A 393 SITE 1 AC3 6 PRO A 307 LYS A 308 ASP A 311 HIS A 339 SITE 2 AC3 6 PRO A 340 HOH A 382 SITE 1 AC4 6 ARG A 172 GLY A 175 LEU A 254 GLY A 278 SITE 2 AC4 6 PHE A 291 ALA A 292 CRYST1 148.550 44.000 47.240 90.00 100.42 90.00 C 1 2 1 4 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 0.006732 0.000000 0.001238 0.00000 SCALE2 0.000000 0.022727 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021524 0.00000