HEADER TRANSFERASE 22-DEC-16 5MRD TITLE HUMAN PDK1-PKCIOTA KINASE CHIMERA IN COMPLEX WITH ALLOSTERIC COMPOUND TITLE 2 PS267 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.M.ARENCIBIA,W.FROEHNER,M.KRUPA,D.PASTOR-FLORES,P.MERKER, AUTHOR 2 T.OELLERICH,S.NEIMANIS,C.SCHMITHALS,V.KOEBERLE,E.SUESS,S.ZEUZEM, AUTHOR 3 H.STARK,A.PIIPER,D.ODADZIC,J.O.SCHULZE,R.M.BIONDI REVDAT 5 17-JAN-24 5MRD 1 REMARK REVDAT 4 16-OCT-19 5MRD 1 REMARK REVDAT 3 01-MAR-17 5MRD 1 JRNL REVDAT 2 25-JAN-17 5MRD 1 JRNL REVDAT 1 18-JAN-17 5MRD 0 JRNL AUTH J.M.ARENCIBIA,W.FROHNER,M.KRUPA,D.PASTOR-FLORES,P.MERKER, JRNL AUTH 2 T.OELLERICH,S.NEIMANIS,C.SCHMITHALS,V.KOBERLE,E.SU,S.ZEUZEM, JRNL AUTH 3 H.STARK,A.PIIPER,D.ODADZIC,J.O.SCHULZE,R.M.BIONDI JRNL TITL AN ALLOSTERIC INHIBITOR SCAFFOLD TARGETING THE PIF-POCKET OF JRNL TITL 2 ATYPICAL PROTEIN KINASE C ISOFORMS. JRNL REF ACS CHEM. BIOL. V. 12 564 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28045490 JRNL DOI 10.1021/ACSCHEMBIO.6B00827 REMARK 2 REMARK 2 RESOLUTION. 1.41 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 57631 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2882 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 46.7974 - 3.8892 0.98 2735 144 0.1479 0.1521 REMARK 3 2 3.8892 - 3.0871 0.97 2655 140 0.1364 0.1563 REMARK 3 3 3.0871 - 2.6969 0.97 2636 139 0.1429 0.1736 REMARK 3 4 2.6969 - 2.4504 0.98 2643 139 0.1384 0.1760 REMARK 3 5 2.4504 - 2.2747 0.98 2645 139 0.1208 0.1535 REMARK 3 6 2.2747 - 2.1406 0.98 2642 139 0.1138 0.1758 REMARK 3 7 2.1406 - 2.0334 0.98 2604 137 0.1189 0.1484 REMARK 3 8 2.0334 - 1.9449 0.98 2625 139 0.1215 0.1599 REMARK 3 9 1.9449 - 1.8700 0.98 2598 136 0.1192 0.1620 REMARK 3 10 1.8700 - 1.8055 0.97 2597 137 0.1321 0.1630 REMARK 3 11 1.8055 - 1.7490 0.98 2629 138 0.1302 0.1713 REMARK 3 12 1.7490 - 1.6990 0.97 2582 136 0.1361 0.1976 REMARK 3 13 1.6990 - 1.6543 0.97 2561 135 0.1453 0.2074 REMARK 3 14 1.6543 - 1.6140 0.97 2624 138 0.1496 0.2282 REMARK 3 15 1.6140 - 1.5773 0.97 2598 137 0.1499 0.2092 REMARK 3 16 1.5773 - 1.5437 0.97 2561 135 0.1625 0.2234 REMARK 3 17 1.5437 - 1.5128 0.96 2587 136 0.1716 0.2309 REMARK 3 18 1.5128 - 1.4843 0.96 2519 133 0.1770 0.2579 REMARK 3 19 1.4843 - 1.4578 0.96 2586 136 0.2067 0.2395 REMARK 3 20 1.4578 - 1.4330 0.96 2575 135 0.2228 0.2641 REMARK 3 21 1.4330 - 1.4099 0.96 2547 134 0.2441 0.2781 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.610 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 : 0.010 2532 REMARK 3 ANGLE : 1.610 3471 REMARK 3 CHIRALITY : 0.097 382 REMARK 3 PLANARITY : 0.009 437 REMARK 3 DIHEDRAL : 16.413 972 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 5MRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002896. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-12 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57639 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 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 (%): 43.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, REMARK 280 10 MM 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 74.55500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.55500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.24000 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: 1330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 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 465 ARG A 75 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 78 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 83 NZ REMARK 470 GLU A 114 CD OE1 OE2 REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 117 ND1 CD2 CE1 NE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 LYS A 123 CD CE NZ REMARK 470 ILE A 124 CD1 REMARK 470 LYS A 173 CE NZ REMARK 470 LYS A 199 CE NZ REMARK 470 LYS A 235 CE NZ REMARK 470 LYS A 257 CD CE NZ REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 304 CD CE NZ 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 HZ3 LYS A 261 OE2 GLU A 328 1.54 REMARK 500 HZ1 LYS A 261 O HOH A 502 1.54 REMARK 500 O HOH A 708 O HOH A 751 2.10 REMARK 500 O HOH A 576 O HOH A 760 2.14 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 OG SER A 105 O GLU A 348 2555 2.08 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 74.32 -150.75 REMARK 500 ARG A 204 -10.58 77.26 REMARK 500 ASP A 223 73.90 74.21 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 827 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 828 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 829 DISTANCE = 6.49 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 S26 A 401 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue S26 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTT 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 DMS A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP A 405 DBREF 5MRD A 50 359 UNP O15530 PDPK1_HUMAN 50 359 SEQADV 5MRD SER A 76 UNP O15530 LYS 76 ENGINEERED MUTATION SEQADV 5MRD VAL A 113 UNP O15530 LEU 113 ENGINEERED MUTATION SEQADV 5MRD VAL A 118 UNP O15530 ILE 118 ENGINEERED MUTATION SEQADV 5MRD ASN A 119 UNP O15530 ILE 119 ENGINEERED MUTATION SEQADV 5MRD ILE A 124 UNP O15530 VAL 124 ENGINEERED MUTATION SEQADV 5MRD GLN A 128 UNP O15530 THR 128 ENGINEERED MUTATION SEQADV 5MRD LYS A 131 UNP O15530 ARG 131 ENGINEERED MUTATION SEQADV 5MRD CYS A 148 UNP O15530 THR 148 ENGINEERED MUTATION SEQADV 5MRD GLY A 288 UNP O15530 TYR 288 CONFLICT SEQADV 5MRD ALA A 292 UNP O15530 GLN 292 CONFLICT SEQRES 1 A 310 ALA MET ASP GLY THR ALA ALA GLU PRO ARG PRO GLY ALA SEQRES 2 A 310 GLY SER LEU GLN HIS ALA GLN PRO PRO PRO GLN PRO ARG SEQRES 3 A 310 SER LYS ARG PRO GLU ASP PHE LYS PHE GLY LYS ILE LEU SEQRES 4 A 310 GLY GLU GLY SER PHE SER THR VAL VAL LEU ALA ARG GLU SEQRES 5 A 310 LEU ALA THR SER ARG GLU TYR ALA ILE LYS ILE VAL GLU SEQRES 6 A 310 LYS ARG HIS VAL ASN LYS GLU ASN LYS ILE PRO TYR VAL SEQRES 7 A 310 GLN ARG GLU LYS ASP VAL MET SER ARG LEU ASP HIS PRO SEQRES 8 A 310 PHE PHE VAL LYS LEU TYR PHE CYS PHE GLN ASP ASP GLU SEQRES 9 A 310 LYS LEU TYR PHE GLY LEU SER TYR ALA LYS ASN GLY GLU SEQRES 10 A 310 LEU LEU LYS TYR ILE ARG LYS ILE GLY SER PHE ASP GLU SEQRES 11 A 310 THR CYS THR ARG PHE TYR THR ALA GLU ILE VAL SER ALA SEQRES 12 A 310 LEU GLU TYR LEU HIS GLY LYS GLY ILE ILE HIS ARG ASP SEQRES 13 A 310 LEU LYS PRO GLU ASN ILE LEU LEU ASN GLU ASP MET HIS SEQRES 14 A 310 ILE GLN ILE THR ASP PHE GLY THR ALA LYS VAL LEU SER SEQRES 15 A 310 PRO GLU SER LYS GLN ALA ARG ALA ASN SEP PHE VAL GLY SEQRES 16 A 310 THR ALA GLN TYR VAL SER PRO GLU LEU LEU THR GLU LYS SEQRES 17 A 310 SER ALA CYS LYS SER SER ASP LEU TRP ALA LEU GLY CYS SEQRES 18 A 310 ILE ILE TYR GLN LEU VAL ALA GLY LEU PRO PRO PHE ARG SEQRES 19 A 310 ALA GLY ASN GLU GLY LEU ILE PHE ALA LYS ILE ILE LYS SEQRES 20 A 310 LEU GLU TYR ASP PHE PRO GLU LYS PHE PHE PRO LYS ALA SEQRES 21 A 310 ARG ASP LEU VAL GLU LYS LEU LEU VAL LEU ASP ALA THR SEQRES 22 A 310 LYS ARG LEU GLY CYS GLU GLU MET GLU GLY TYR GLY PRO SEQRES 23 A 310 LEU LYS ALA HIS PRO PHE PHE GLU SER VAL THR TRP GLU SEQRES 24 A 310 ASN LEU HIS GLN GLN THR PRO PRO LYS LEU THR MODRES 5MRD SEP A 241 SER MODIFIED RESIDUE HET SEP A 241 14 HET S26 A 401 23 HET DTT A 402 18 HET DMS A 403 10 HET DMS A 404 10 HET ATP A 405 43 HETNAM SEP PHOSPHOSERINE HETNAM S26 ETHYL (2~{S})-1-(6-CHLORANYL-1,3-BENZOTHIAZOL-2-YL)-4- HETNAM 2 S26 OXIDANYL-5-OXIDANYLIDENE-2-THIOPHEN-2-YL-2~{H}- HETNAM 3 S26 PYRROLE-3-CARBOXYLATE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETNAM DMS DIMETHYL SULFOXIDE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETSYN SEP PHOSPHONOSERINE HETSYN S26 PS267 HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 S26 C18 H13 CL N2 O4 S2 FORMUL 3 DTT C4 H10 O2 S2 FORMUL 4 DMS 2(C2 H6 O S) FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 HOH *329(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 LEU A 297 1 12 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 ASN A 349 GLN A 353 5 5 SHEET 1 AA1 5 PHE A 82 GLU A 90 0 SHEET 2 AA1 5 SER A 94 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 149 O TYR A 156 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 1.33 SITE 1 AC1 8 VAL A 118 ASN A 119 ILE A 124 GLN A 128 SITE 2 AC1 8 LYS A 131 GLN A 150 LEU A 155 HOH A 557 SITE 1 AC2 7 GLY A 244 ALA A 246 ARG A 283 GLU A 287 SITE 2 AC2 7 ASP A 300 PRO A 302 HOH A 666 SITE 1 AC3 9 THR A 104 SER A 105 HIS A 139 TRP A 347 SITE 2 AC3 9 GLU A 348 ASN A 349 LEU A 350 HIS A 351 SITE 3 AC3 9 HOH A 604 SITE 1 AC4 3 PRO A 79 PHE A 82 PHE A 84 SITE 1 AC5 14 LEU A 88 GLY A 89 SER A 94 VAL A 96 SITE 2 AC5 14 LYS A 111 TYR A 126 SER A 160 ALA A 162 SITE 3 AC5 14 GLU A 166 LEU A 212 ASP A 223 HOH A 519 SITE 4 AC5 14 HOH A 556 HOH A 693 CRYST1 149.110 44.480 47.810 90.00 101.96 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 0.006706 0.000000 0.001421 0.00000 SCALE2 0.000000 0.022482 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021380 0.00000