HEADER TRANSFERASE 14-SEP-16 5LVO TITLE HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND PSE10 TITLE 2 BOUND TO THE PIF-POCKET COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HPDK1; 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 GENE: PDPK1, PDK1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS PROTEIN KINASE, ALLOSTERIC REGULATION, SMALL COMPOUNDS, PIF-POCKET, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.O.SCHULZE,G.SALADINO,K.BUSSCHOTS,S.NEIMANIS,E.SUESS,D.ODADZIC, AUTHOR 2 S.ZEUZEM,V.HINDIE,A.K.HERBRAND,M.N.LISA,P.M.ALZARI,F.L.GERVASIO, AUTHOR 3 R.M.BIONDI REVDAT 4 17-JAN-24 5LVO 1 REMARK REVDAT 3 16-OCT-19 5LVO 1 REMARK REVDAT 2 02-NOV-16 5LVO 1 JRNL REVDAT 1 19-OCT-16 5LVO 0 JRNL AUTH J.O.SCHULZE,G.SALADINO,K.BUSSCHOTS,S.NEIMANIS,E.SU, JRNL AUTH 2 D.ODADZIC,S.ZEUZEM,V.HINDIE,A.K.HERBRAND,M.N.LISA, JRNL AUTH 3 P.M.ALZARI,F.L.GERVASIO,R.M.BIONDI JRNL TITL BIDIRECTIONAL ALLOSTERIC COMMUNICATION BETWEEN THE JRNL TITL 2 ATP-BINDING SITE AND THE REGULATORY PIF POCKET IN PDK1 JRNL TITL 3 PROTEIN KINASE. JRNL REF CELL CHEM BIOL V. 23 1193 2016 JRNL REFN ESSN 2451-9456 JRNL PMID 27693059 JRNL DOI 10.1016/J.CHEMBIOL.2016.06.017 REMARK 2 REMARK 2 RESOLUTION. 1.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 126719 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.135 REMARK 3 FREE R VALUE : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6337 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 72.7024 - 2.3482 0.99 12231 644 0.1395 0.1502 REMARK 3 2 2.3482 - 1.8638 1.00 12146 640 0.1119 0.1371 REMARK 3 3 1.8638 - 1.6282 1.00 12064 634 0.1081 0.1382 REMARK 3 4 1.6282 - 1.4793 1.00 12059 635 0.1013 0.1379 REMARK 3 5 1.4793 - 1.3733 1.00 12029 633 0.1169 0.1473 REMARK 3 6 1.3733 - 1.2923 1.00 12003 632 0.1343 0.1669 REMARK 3 7 1.2923 - 1.2276 1.00 11977 630 0.1569 0.1889 REMARK 3 8 1.2276 - 1.1741 1.00 12005 632 0.1824 0.1970 REMARK 3 9 1.1741 - 1.1289 1.00 11971 630 0.2078 0.2316 REMARK 3 10 1.1289 - 1.0900 1.00 11897 627 0.2481 0.2684 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.630 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) : 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 2513 REMARK 3 ANGLE : 1.702 3436 REMARK 3 CHIRALITY : 0.114 383 REMARK 3 PLANARITY : 0.012 430 REMARK 3 DIHEDRAL : 17.261 949 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 5LVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-10 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126722 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.090 REMARK 200 RESOLUTION RANGE LOW (A) : 73.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 43.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, REMARK 280 0.01 M DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 74.11000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.11000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.21000 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 TOTAL BURIED SURFACE AREA: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 N CA CB CG CD OE1 NE2 REMARK 470 ARG A 75 CD NE CZ NH1 NH2 REMARK 470 LYS A 76 CG CD CE NZ REMARK 470 ARG A 78 CD NE CZ NH1 NH2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 SER A 92 OG REMARK 470 PHE A 93 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 100 NE 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 CG CD OE1 OE2 REMARK 470 LYS A 123 CE NZ REMARK 470 ARG A 131 CZ NH1 NH2 REMARK 470 LYS A 144 CD CE NZ REMARK 470 LYS A 163 CE NZ REMARK 470 ARG A 172 CD NE CZ NH1 NH2 REMARK 470 LYS A 199 CE NZ REMARK 470 LYS A 235 CE NZ REMARK 470 LYS A 257 CD CE NZ REMARK 470 LYS A 293 CE NZ REMARK 470 LYS A 296 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 LYS A 357 CD CE NZ 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 HD22 ASN A 122 O HOH A 509 1.46 REMARK 500 O1G ATP A 401 O HOH A 501 2.06 REMARK 500 O GLU A 348 O HOH A 502 2.07 REMARK 500 O HOH A 821 O HOH A 859 2.08 REMARK 500 O HOH A 854 O HOH A 859 2.17 REMARK 500 OE1 GLU A 331 O HOH A 504 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 704 O HOH A 762 2555 1.93 REMARK 500 REMARK 500 REMARK: NULL 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 -0.088 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 106 NE - CZ - NH1 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = 4.1 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 73.64 -155.84 REMARK 500 ARG A 204 -9.82 77.65 REMARK 500 ASP A 223 70.17 79.12 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 A 860 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 861 DISTANCE = 6.11 ANGSTROMS 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 78W A 402 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 78W A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTD A 404 DBREF 5LVO A 50 359 UNP O15530 PDPK1_HUMAN 50 359 SEQADV 5LVO GLY A 49 UNP O15530 EXPRESSION TAG SEQADV 5LVO GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 5LVO 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 5LVO SEP A 241 SER MODIFIED RESIDUE HET SEP A 241 14 HET ATP A 401 42 HET 78W A 402 22 HET DMS A 403 10 HET DTD A 404 8 HET CL A 405 1 HETNAM SEP PHOSPHOSERINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 78W 2-OXIDANYLIDENEPROPYL ~{N}-(2-CHLORANYL-6-FLUORANYL- HETNAM 2 78W PHENYL)CARBONYL-~{N}'-(4-CHLOROPHENYL) HETNAM 3 78W CARBAMIMIDOTHIOATE HETNAM DMS DIMETHYL SULFOXIDE HETNAM DTD DITHIANE DIOL HETNAM CL CHLORIDE ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 78W C17 H13 CL2 F N2 O2 S FORMUL 4 DMS C2 H6 O S FORMUL 5 DTD C4 H8 O2 S2 FORMUL 6 CL CL 1- FORMUL 7 HOH *361(H2 O) HELIX 1 AA1 ARG A 78 GLU A 80 5 3 HELIX 2 AA2 LYS A 115 GLU A 121 1 7 HELIX 3 AA3 LYS A 123 LEU A 137 1 15 HELIX 4 AA4 LEU A 167 GLY A 175 1 9 HELIX 5 AA5 ASP A 178 LYS A 199 1 22 HELIX 6 AA6 LYS A 207 GLU A 209 5 3 HELIX 7 AA7 THR A 245 VAL A 249 5 5 HELIX 8 AA8 SER A 250 LYS A 257 1 8 HELIX 9 AA9 CYS A 260 GLY A 278 1 19 HELIX 10 AB1 ASN A 286 LYS A 296 1 11 HELIX 11 AB2 PHE A 306 LEU A 317 1 12 HELIX 12 AB3 ASP A 320 ARG A 324 5 5 HELIX 13 AB4 CYS A 327 GLU A 331 5 5 HELIX 14 AB5 GLY A 332 ALA A 338 1 7 HELIX 15 AB6 HIS A 339 GLU A 343 5 5 HELIX 16 AB7 THR A 346 GLN A 353 5 8 SHEET 1 AA1 5 PHE A 82 GLU A 90 0 SHEET 2 AA1 5 THR A 95 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 AA1 5 GLU A 107 GLU A 114 -1 O ILE A 112 N THR A 95 SHEET 4 AA1 5 LYS A 154 LEU A 159 -1 O LEU A 159 N ALA A 109 SHEET 5 AA1 5 LEU A 145 GLN A 150 -1 N PHE A 147 O GLY A 158 SHEET 1 AA2 3 GLY A 165 GLU A 166 0 SHEET 2 AA2 3 ILE A 211 LEU A 213 -1 O LEU A 213 N GLY A 165 SHEET 3 AA2 3 ILE A 219 ILE A 221 -1 O GLN A 220 N LEU A 212 SHEET 1 AA3 2 ILE A 201 ILE A 202 0 SHEET 2 AA3 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 1.32 SITE 1 AC1 22 GLY A 89 GLY A 91 SER A 92 SER A 94 SITE 2 AC1 22 VAL A 96 ALA A 109 LYS A 111 SER A 160 SITE 3 AC1 22 ALA A 162 GLU A 166 LEU A 212 HOH A 501 SITE 4 AC1 22 HOH A 507 HOH A 513 HOH A 515 HOH A 538 SITE 5 AC1 22 HOH A 588 HOH A 608 HOH A 621 HOH A 669 SITE 6 AC1 22 HOH A 710 HOH A 779 SITE 1 AC2 8 ILE A 119 VAL A 127 THR A 128 THR A 148 SITE 2 AC2 8 PHE A 149 GLN A 150 TYR A 156 PHE A 157 SITE 1 AC3 8 THR A 104 SER A 105 HIS A 139 TRP A 347 SITE 2 AC3 8 GLU A 348 ASN A 349 LEU A 350 HIS A 351 SITE 1 AC4 6 PHE A 242 VAL A 243 GLY A 244 THR A 245 SITE 2 AC4 6 ALA A 246 ARG A 283 CRYST1 148.220 44.420 47.870 90.00 101.81 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 0.006747 0.000000 0.001411 0.00000 SCALE2 0.000000 0.022512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021342 0.00000