HEADER TRANSFERASE 17-AUG-15 5ACK TITLE HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND 7 BOUND TITLE 2 TO THE PIF-POCKET COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 50-359; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFASTBAC KEYWDS TRANSFERASE, KINASE, ALLOSTERY, VIRTUAL SCREENING, PHARMACOPHORE, KEYWDS 2 MULTICOMPONENT REACTION EXPDTA X-RAY DIFFRACTION AUTHOR J.O.SCHULZE,E.KROON,A.DOEMLING,R.M.BIONDI REVDAT 3 10-JAN-24 5ACK 1 REMARK LINK REVDAT 2 27-JAN-16 5ACK 1 JRNL REVDAT 1 21-OCT-15 5ACK 0 JRNL AUTH E.KROON,J.O.SCHULZE,E.SUSS,C.J.CAMACHO,R.M.BIONDI,A.DOMLING JRNL TITL DISCOVERY OF A POTENT ALLOSTERIC KINASE MODULATOR BY JRNL TITL 2 COMBINING COMPUTATIONAL AND SYNTHETIC METHODS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 13933 2015 JRNL REFN ISSN 1433-7851 JRNL PMID 26385475 JRNL DOI 10.1002/ANIE.201506310 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 83257 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.143 REMARK 3 R VALUE (WORKING SET) : 0.142 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4164 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 72.6924 - 3.8525 0.96 2758 146 0.1496 0.1443 REMARK 3 2 3.8525 - 3.0578 0.96 2695 141 0.1409 0.1748 REMARK 3 3 3.0578 - 2.6713 0.97 2682 142 0.1438 0.1674 REMARK 3 4 2.6713 - 2.4270 0.97 2670 140 0.1390 0.1516 REMARK 3 5 2.4270 - 2.2530 0.97 2685 141 0.1205 0.1442 REMARK 3 6 2.2530 - 2.1202 0.96 2665 141 0.1150 0.1327 REMARK 3 7 2.1202 - 2.0140 0.97 2695 142 0.1200 0.1699 REMARK 3 8 2.0140 - 1.9263 0.97 2627 138 0.1197 0.1424 REMARK 3 9 1.9263 - 1.8522 0.97 2662 140 0.1270 0.1533 REMARK 3 10 1.8522 - 1.7883 0.98 2702 142 0.1271 0.1525 REMARK 3 11 1.7883 - 1.7323 0.97 2677 141 0.1222 0.1521 REMARK 3 12 1.7323 - 1.6828 0.97 2633 139 0.1218 0.1709 REMARK 3 13 1.6828 - 1.6385 0.97 2656 139 0.1205 0.1615 REMARK 3 14 1.6385 - 1.5985 0.97 2626 139 0.1239 0.1557 REMARK 3 15 1.5985 - 1.5622 0.96 2644 139 0.1231 0.1726 REMARK 3 16 1.5622 - 1.5289 0.96 2623 138 0.1306 0.1640 REMARK 3 17 1.5289 - 1.4983 0.96 2638 139 0.1372 0.1865 REMARK 3 18 1.4983 - 1.4701 0.96 2652 139 0.1398 0.1697 REMARK 3 19 1.4701 - 1.4438 0.96 2584 136 0.1593 0.1901 REMARK 3 20 1.4438 - 1.4193 0.96 2642 139 0.1711 0.2132 REMARK 3 21 1.4193 - 1.3964 0.96 2614 138 0.1768 0.2060 REMARK 3 22 1.3964 - 1.3750 0.95 2631 138 0.1811 0.2106 REMARK 3 23 1.3750 - 1.3547 0.96 2571 136 0.1893 0.2422 REMARK 3 24 1.3547 - 1.3356 0.95 2587 136 0.1954 0.2252 REMARK 3 25 1.3356 - 1.3176 0.95 2598 137 0.2150 0.2558 REMARK 3 26 1.3176 - 1.3005 0.95 2594 136 0.2267 0.2649 REMARK 3 27 1.3005 - 1.2842 0.95 2594 137 0.2440 0.2743 REMARK 3 28 1.2842 - 1.2688 0.95 2568 135 0.2498 0.2750 REMARK 3 29 1.2688 - 1.2540 0.95 2585 136 0.2586 0.2721 REMARK 3 30 1.2540 - 1.2399 0.93 2535 134 0.2758 0.3086 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.016 2580 REMARK 3 ANGLE : 1.762 3543 REMARK 3 CHIRALITY : 0.105 392 REMARK 3 PLANARITY : 0.011 446 REMARK 3 DIHEDRAL : 14.278 993 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5ACK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1290064700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-14 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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SI-111 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 73.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: PDB ENTRY 3HRC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, REMARK 280 0.01 M DTT 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 73.99000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.27000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.99000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.27000 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 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 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 GLN A 73 CG CD OE1 NE2 REMARK 470 ARG A 75 NE CZ NH1 NH2 REMARK 470 LYS A 76 CD CE NZ REMARK 470 ARG A 78 NE CZ NH1 NH2 REMARK 470 LYS A 83 NZ REMARK 470 SER A 92 OG REMARK 470 PHE A 93 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 100 CZ NH1 NH2 REMARK 470 ARG A 116 CD NE CZ NH1 NH2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 121 CD OE1 OE2 REMARK 470 LYS A 123 CE NZ REMARK 470 ARG A 131 NE CZ NH1 NH2 REMARK 470 LYS A 163 CE NZ REMARK 470 ARG A 172 NE CZ NH1 NH2 REMARK 470 LYS A 173 CD CE NZ REMARK 470 GLU A 215 CD OE1 OE2 REMARK 470 LYS A 235 CE NZ REMARK 470 LYS A 257 CE NZ REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 304 CD CE NZ REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 ASN A 349 CG OD1 ND2 REMARK 470 GLN A 352 OE1 NE2 REMARK 470 LYS A 357 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 160 CB SER A 160 OG -0.091 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (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,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 183 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES 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 74.89 -153.06 REMARK 500 SER A 176 144.74 179.86 REMARK 500 ARG A 204 -12.73 78.01 REMARK 500 ASP A 223 73.44 79.29 REMARK 500 ASP A 223 79.01 72.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2032 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A2038 DISTANCE = 6.52 ANGSTROMS REMARK 525 HOH A2050 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A2154 DISTANCE = 5.97 ANGSTROMS 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 NA A 902 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 210 OD1 REMARK 620 2 HOH A2181 O 76.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 900 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 223 OD2 REMARK 620 2 ATP A 500 O1A 116.3 REMARK 620 3 ATP A 500 O2B 78.8 85.2 REMARK 620 4 ATP A 500 O3G 128.0 108.0 79.1 REMARK 620 5 HOH A2022 O 132.9 74.8 147.5 83.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 901 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 244 O REMARK 620 2 THR A 245 OG1 80.6 REMARK 620 3 HOH A2220 O 84.9 101.6 REMARK 620 4 HOH A2221 O 55.9 135.9 71.0 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 ATP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SVQ A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTD A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 900 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 902 DBREF 5ACK A 50 359 UNP O15530 PDPK1_HUMAN 50 359 SEQADV 5ACK GLY A 49 UNP O15530 EXPRESSION TAG SEQADV 5ACK GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 5ACK 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 5ACK SEP A 241 SER PHOSPHOSERINE HET SEP A 241 14 HET ATP A 500 35 HET SVQ A 600 52 HET DTD A 700 8 HET DMS A 800 10 HET NA A 900 1 HET NA A 901 1 HET NA A 902 2 HETNAM SEP PHOSPHOSERINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM SVQ 1-(4-CHLOROPHENETHYL)-2-(2-CHLOROPHENYL)-6- HETNAM 2 SVQ OXOPIPERIDINE-3-CARBOXYLIC ACID HETNAM DTD DITHIANE DIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM NA SODIUM ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 SVQ C20 H19 CL2 N O3 FORMUL 4 DTD C4 H8 O2 S2 FORMUL 5 DMS C2 H6 O S FORMUL 6 NA 3(NA 1+) FORMUL 9 HOH *332(H2 O) HELIX 1 1 LYS A 115 GLU A 121 1 7 HELIX 2 2 VAL A 124 SER A 135 1 12 HELIX 3 3 LEU A 167 ILE A 174 1 8 HELIX 4 4 GLU A 179 LYS A 199 1 21 HELIX 5 5 PRO A 251 GLU A 256 1 6 HELIX 6 6 SER A 262 ALA A 277 1 16 HELIX 7 7 GLU A 287 ILE A 295 1 9 HELIX 8 8 PRO A 307 LEU A 316 1 10 HELIX 9 9 TYR A 333 ALA A 338 1 6 SHEET 1 A 5 PHE A 82 GLY A 91 0 SHEET 2 A 5 SER A 94 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 A 5 ARG A 106 GLU A 114 -1 O ILE A 110 N VAL A 97 SHEET 4 A 5 LYS A 154 SER A 160 -1 O LEU A 159 N ALA A 109 SHEET 5 A 5 PHE A 147 ASP A 151 -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 ASN A 214 -1 O LEU A 213 N GLY A 165 SHEET 3 B 3 HIS A 218 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 1.34 LINK C SEP A 241 N PHE A 242 1555 1555 1.32 LINK OD1 ASN A 210 NA A NA A 902 1555 1555 2.32 LINK OD1 ASN A 210 NA B NA A 902 1555 1555 2.86 LINK OD2BASP A 223 NA NA A 900 1555 1555 2.24 LINK O GLY A 244 NA NA A 901 1555 1555 2.62 LINK OG1 THR A 245 NA NA A 901 1555 1555 2.74 LINK O1A ATP A 500 NA NA A 900 1555 1555 2.42 LINK O2B ATP A 500 NA NA A 900 1555 1555 2.16 LINK O3G ATP A 500 NA NA A 900 1555 1555 2.46 LINK NA NA A 900 O HOH A2022 1555 1555 2.47 LINK NA NA A 901 O HOH A2220 1555 1555 2.44 LINK NA NA A 901 O HOH A2221 1555 1555 2.16 LINK NA A NA A 902 O HOH A2181 1555 1555 3.09 SITE 1 AC1 21 GLY A 89 GLU A 90 GLY A 91 SER A 92 SITE 2 AC1 21 SER A 94 VAL A 96 ALA A 109 SER A 160 SITE 3 AC1 21 TYR A 161 ALA A 162 GLU A 166 LEU A 212 SITE 4 AC1 21 NA A 900 NA A 902 HOH A2020 HOH A2022 SITE 5 AC1 21 HOH A2189 HOH A2190 HOH A2330 HOH A2331 SITE 6 AC1 21 HOH A2332 SITE 1 AC2 7 LYS A 115 VAL A 127 ARG A 131 THR A 148 SITE 2 AC2 7 PHE A 149 GLN A 150 LEU A 155 SITE 1 AC3 6 PHE A 242 VAL A 243 GLY A 244 GLU A 287 SITE 2 AC3 6 PHE A 291 HOH A2221 SITE 1 AC4 9 THR A 104 SER A 105 HIS A 139 PHE A 141 SITE 2 AC4 9 TRP A 347 ASN A 349 LEU A 350 HIS A 351 SITE 3 AC4 9 HOH A2027 SITE 1 AC5 4 ASP A 223 ATP A 500 NA A 902 HOH A2022 SITE 1 AC6 4 GLY A 244 THR A 245 HOH A2220 HOH A2221 SITE 1 AC7 5 ASN A 210 ASP A 223 ATP A 500 NA A 900 SITE 2 AC7 5 HOH A2181 CRYST1 147.980 44.540 47.810 90.00 101.25 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 0.006758 0.000000 0.001344 0.00000 SCALE2 0.000000 0.022452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021326 0.00000