HEADER TRANSFERASE 14-SEP-16 5LVL TITLE HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH COMPOUND PS653 BOUND TO THE TITLE 2 ATP-BINDING SITE 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 5LVL 1 REMARK REVDAT 3 16-OCT-19 5LVL 1 REMARK ATOM REVDAT 2 02-NOV-16 5LVL 1 JRNL REVDAT 1 19-OCT-16 5LVL 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. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 59735 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2987 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 73.0158 - 3.8621 1.00 2810 148 0.1591 0.1849 REMARK 3 2 3.8621 - 3.0654 1.00 2739 145 0.1433 0.1496 REMARK 3 3 3.0654 - 2.6779 1.00 2724 143 0.1472 0.1648 REMARK 3 4 2.6779 - 2.4331 1.00 2720 143 0.1457 0.1975 REMARK 3 5 2.4331 - 2.2587 1.00 2705 142 0.1270 0.1464 REMARK 3 6 2.2587 - 2.1255 1.00 2705 143 0.1258 0.1600 REMARK 3 7 2.1255 - 2.0190 1.00 2695 142 0.1281 0.1562 REMARK 3 8 2.0190 - 1.9311 1.00 2702 142 0.1347 0.1673 REMARK 3 9 1.9311 - 1.8568 1.00 2682 141 0.1410 0.1775 REMARK 3 10 1.8568 - 1.7927 1.00 2723 143 0.1506 0.1658 REMARK 3 11 1.7927 - 1.7367 1.00 2682 141 0.1477 0.2043 REMARK 3 12 1.7367 - 1.6870 1.00 2681 142 0.1470 0.1694 REMARK 3 13 1.6870 - 1.6426 1.00 2702 142 0.1584 0.1807 REMARK 3 14 1.6426 - 1.6025 1.00 2706 142 0.1634 0.2058 REMARK 3 15 1.6025 - 1.5661 1.00 2712 143 0.1715 0.1921 REMARK 3 16 1.5661 - 1.5327 1.00 2634 139 0.1873 0.2258 REMARK 3 17 1.5327 - 1.5021 1.00 2714 142 0.2031 0.2143 REMARK 3 18 1.5021 - 1.4737 1.00 2652 140 0.2148 0.2522 REMARK 3 19 1.4737 - 1.4474 1.00 2695 142 0.2351 0.2293 REMARK 3 20 1.4474 - 1.4229 1.00 2713 143 0.2476 0.2852 REMARK 3 21 1.4229 - 1.3999 1.00 2652 139 0.2527 0.2540 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.850 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 : 0.013 2627 REMARK 3 ANGLE : 1.566 3583 REMARK 3 CHIRALITY : 0.094 389 REMARK 3 PLANARITY : 0.010 456 REMARK 3 DIHEDRAL : 12.696 1042 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 74 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.5138 2.8712 -15.6099 REMARK 3 T TENSOR REMARK 3 T11: 0.1779 T22: 0.2943 REMARK 3 T33: 0.1362 T12: 0.0315 REMARK 3 T13: -0.0088 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 5.3988 L22: 5.4966 REMARK 3 L33: 4.1140 L12: -0.0083 REMARK 3 L13: -0.3473 L23: 0.0033 REMARK 3 S TENSOR REMARK 3 S11: 0.1062 S12: 0.0281 S13: 0.6087 REMARK 3 S21: 0.0849 S22: -0.1067 S23: -0.0495 REMARK 3 S31: -0.3674 S32: 0.0198 S33: -0.0185 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 120 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3888 3.5609 -14.3848 REMARK 3 T TENSOR REMARK 3 T11: 0.1553 T22: 0.2712 REMARK 3 T33: 0.1112 T12: 0.0656 REMARK 3 T13: 0.0013 T23: 0.0248 REMARK 3 L TENSOR REMARK 3 L11: 3.2234 L22: 3.1669 REMARK 3 L33: 2.0506 L12: -0.2076 REMARK 3 L13: 0.9861 L23: -0.4236 REMARK 3 S TENSOR REMARK 3 S11: 0.0660 S12: 0.3903 S13: 0.1551 REMARK 3 S21: -0.1796 S22: -0.0952 S23: 0.2581 REMARK 3 S31: -0.2967 S32: -0.1786 S33: -0.0320 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 121 THROUGH 136 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.6762 12.4462 -3.9551 REMARK 3 T TENSOR REMARK 3 T11: 0.3283 T22: 0.3992 REMARK 3 T33: 0.3004 T12: 0.1227 REMARK 3 T13: 0.0907 T23: 0.0347 REMARK 3 L TENSOR REMARK 3 L11: 4.9479 L22: 5.0766 REMARK 3 L33: 6.7825 L12: -1.5864 REMARK 3 L13: 2.2123 L23: -2.8833 REMARK 3 S TENSOR REMARK 3 S11: 0.4270 S12: 0.6529 S13: 0.2896 REMARK 3 S21: -0.2850 S22: -0.3686 S23: 0.1695 REMARK 3 S31: -0.5070 S32: -0.5041 S33: 0.0037 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 137 THROUGH 178 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.8738 -3.2847 -5.1713 REMARK 3 T TENSOR REMARK 3 T11: 0.1081 T22: 0.1217 REMARK 3 T33: 0.0980 T12: 0.0292 REMARK 3 T13: 0.0036 T23: -0.0067 REMARK 3 L TENSOR REMARK 3 L11: 1.8829 L22: 1.8972 REMARK 3 L33: 2.2445 L12: 1.1553 REMARK 3 L13: -1.1564 L23: -1.0587 REMARK 3 S TENSOR REMARK 3 S11: -0.0989 S12: 0.1868 S13: -0.0188 REMARK 3 S21: -0.2616 S22: 0.0789 S23: -0.0068 REMARK 3 S31: 0.0321 S32: -0.0593 S33: 0.0060 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 179 THROUGH 260 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.6522 1.0605 6.2165 REMARK 3 T TENSOR REMARK 3 T11: 0.0773 T22: 0.0830 REMARK 3 T33: 0.0785 T12: -0.0105 REMARK 3 T13: 0.0026 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.3321 L22: 1.8002 REMARK 3 L33: 1.0342 L12: -0.0479 REMARK 3 L13: 0.0933 L23: -0.1446 REMARK 3 S TENSOR REMARK 3 S11: -0.0079 S12: 0.0293 S13: 0.1496 REMARK 3 S21: -0.0445 S22: -0.0127 S23: -0.0172 REMARK 3 S31: -0.1034 S32: 0.0301 S33: 0.0089 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 261 THROUGH 327 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.2475 -7.0343 10.3743 REMARK 3 T TENSOR REMARK 3 T11: 0.0815 T22: 0.1004 REMARK 3 T33: 0.1143 T12: -0.0131 REMARK 3 T13: 0.0059 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 1.2923 L22: 1.9748 REMARK 3 L33: 1.3583 L12: -0.2609 REMARK 3 L13: 0.3822 L23: -0.0411 REMARK 3 S TENSOR REMARK 3 S11: 0.0293 S12: -0.1123 S13: -0.1231 REMARK 3 S21: 0.0551 S22: 0.0115 S23: 0.2114 REMARK 3 S31: 0.0821 S32: -0.1370 S33: -0.0215 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 328 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.1489 -10.9127 15.5227 REMARK 3 T TENSOR REMARK 3 T11: 0.1173 T22: 0.1327 REMARK 3 T33: 0.1220 T12: 0.0021 REMARK 3 T13: -0.0232 T23: 0.0322 REMARK 3 L TENSOR REMARK 3 L11: 2.9326 L22: 2.6129 REMARK 3 L33: 2.6245 L12: -1.0832 REMARK 3 L13: -0.7981 L23: 0.5816 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: -0.1078 S13: -0.2050 REMARK 3 S21: 0.0670 S22: -0.0205 S23: -0.1764 REMARK 3 S31: 0.1223 S32: 0.1580 S33: 0.0320 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 5LVL 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_1200001423. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-11 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 : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59735 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 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 (%): 43.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 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 74.12000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.21500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.12000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.21500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 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 563 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 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 HG SER A 105 O GLU A 348 2555 1.31 REMARK 500 OG SER A 105 O GLU A 348 2555 1.96 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 151 -165.51 -129.05 REMARK 500 ARG A 204 -12.89 78.34 REMARK 500 ASP A 223 78.29 78.07 REMARK 500 SER A 344 3.54 82.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 537 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTD 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 DMS A 405 DBREF 5LVL A 50 359 UNP O15530 PDPK1_HUMAN 50 359 SEQADV 5LVL GLY A 49 UNP O15530 EXPRESSION TAG SEQADV 5LVL GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 5LVL 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 5LVL SEP A 241 SER MODIFIED RESIDUE HET SEP A 241 14 HET 537 A 401 17 HET DTD A 402 8 HET DMS A 403 20 HET DMS A 404 10 HET DMS A 405 10 HETNAM SEP PHOSPHOSERINE HETNAM 537 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE HETNAM DTD DITHIANE DIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 537 C14 H8 N2 O FORMUL 3 DTD C4 H8 O2 S2 FORMUL 4 DMS 3(C2 H6 O S) FORMUL 7 HOH *267(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 ARG A 136 1 14 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 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 PHE A 157 N LYS A 111 SHEET 5 AA1 5 LEU A 145 GLN A 150 -1 N TYR A 146 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 1.32 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 SITE 1 AC1 8 LEU A 88 ALA A 109 LEU A 159 SER A 160 SITE 2 AC1 8 TYR A 161 ALA A 162 GLY A 165 LEU A 212 SITE 1 AC2 8 PHE A 242 VAL A 243 GLY A 244 THR A 245 SITE 2 AC2 8 ALA A 246 GLU A 287 PHE A 291 HOH A 629 SITE 1 AC3 11 THR A 104 SER A 105 HIS A 139 PHE A 141 SITE 2 AC3 11 SER A 191 TRP A 347 GLU A 348 ASN A 349 SITE 3 AC3 11 LEU A 350 HIS A 351 HOH A 542 SITE 1 AC4 5 PHE A 84 ILE A 112 LYS A 154 TYR A 156 SITE 2 AC4 5 GLU A 331 SITE 1 AC5 4 TYR A 299 ASP A 300 PHE A 301 GLU A 314 CRYST1 148.240 44.430 47.250 90.00 100.34 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 0.006746 0.000000 0.001231 0.00000 SCALE2 0.000000 0.022507 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021513 0.00000