HEADER TRANSFERASE 08-SEP-11 4A07 TITLE HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC ACTIVATOR PS171 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 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 50-359; COMPND 5 SYNONYM: HPDK1; COMPND 6 EC: 2.7.11.1; COMPND 7 ENGINEERED: YES; COMPND 8 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_VECTOR: PFASTBAC KEYWDS TRANSFERASE, ALLOSTERIC SITE EXPDTA X-RAY DIFFRACTION AUTHOR J.O.SCHULZE,L.A.LOPEZ-GARCIA,W.FROEHNER,H.ZHANG,J.NAVRATIL,V.HINDIE, AUTHOR 2 S.ZEUZEM,P.M.ALZARI,S.NEIMANIS,M.ENGEL,R.M.BIONDI REVDAT 3 20-DEC-23 4A07 1 REMARK LINK REVDAT 2 21-DEC-11 4A07 1 ATOM REVDAT 1 07-DEC-11 4A07 0 JRNL AUTH L.A.LOPEZ-GARCIA,J.O.SCHULZE,W.FROHNER,H.ZHANG,E.SUSS, JRNL AUTH 2 N.WEBER,J.NAVRATIL,S.AMON,V.HINDIE,S.ZEUZEM,T.J.JORGENSEN, JRNL AUTH 3 P.M.ALZARI,S.NEIMANIS,M.ENGEL,R.M.BIONDI JRNL TITL ALLOSTERIC REGULATION OF PROTEIN KINASE PKCZETA BY THE JRNL TITL 2 N-TERMINAL C1 DOMAIN AND SMALL COMPOUNDS TO THE PIF-POCKET. JRNL REF CHEM.BIOL. V. 18 1463 2011 JRNL REFN ISSN 1074-5521 JRNL PMID 22118680 JRNL DOI 10.1016/J.CHEMBIOL.2011.08.010 REMARK 2 REMARK 2 RESOLUTION. 1.85 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25850 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1292 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 36.2486 - 3.8466 1.00 2840 149 0.1556 0.1883 REMARK 3 2 3.8466 - 3.0536 1.00 2762 145 0.1534 0.1776 REMARK 3 3 3.0536 - 2.6678 1.00 2723 144 0.1587 0.2193 REMARK 3 4 2.6678 - 2.4239 1.00 2740 144 0.1544 0.2038 REMARK 3 5 2.4239 - 2.2502 0.99 2722 143 0.1432 0.1845 REMARK 3 6 2.2502 - 2.1176 0.99 2717 143 0.1467 0.1799 REMARK 3 7 2.1176 - 2.0115 0.99 2692 142 0.1565 0.2333 REMARK 3 8 2.0115 - 1.9240 0.99 2692 141 0.1833 0.2160 REMARK 3 9 1.9240 - 1.8499 0.99 2670 141 0.2261 0.2768 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.43 REMARK 3 B_SOL : 40.29 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58510 REMARK 3 B22 (A**2) : 0.21490 REMARK 3 B33 (A**2) : 0.37020 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.44890 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 2417 REMARK 3 ANGLE : 1.090 3308 REMARK 3 CHIRALITY : 0.074 356 REMARK 3 PLANARITY : 0.005 409 REMARK 3 DIHEDRAL : 13.644 884 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 75:99) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9155 24.5124 -16.1908 REMARK 3 T TENSOR REMARK 3 T11: 0.1035 T22: 0.2100 REMARK 3 T33: 0.1040 T12: 0.0301 REMARK 3 T13: -0.0186 T23: 0.0383 REMARK 3 L TENSOR REMARK 3 L11: 2.2946 L22: 3.0799 REMARK 3 L33: 1.2532 L12: 2.1782 REMARK 3 L13: 0.3919 L23: 0.2411 REMARK 3 S TENSOR REMARK 3 S11: 0.1267 S12: 0.1656 S13: 0.2069 REMARK 3 S21: -0.1657 S22: -0.1322 S23: 0.3011 REMARK 3 S31: 0.0217 S32: -0.2107 S33: -0.0108 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 100:117) REMARK 3 ORIGIN FOR THE GROUP (A): -7.0933 25.6663 -13.9567 REMARK 3 T TENSOR REMARK 3 T11: 0.0679 T22: 0.2026 REMARK 3 T33: 0.0451 T12: 0.0353 REMARK 3 T13: -0.0078 T23: 0.0330 REMARK 3 L TENSOR REMARK 3 L11: 0.1087 L22: 0.2667 REMARK 3 L33: 1.7499 L12: -0.0676 REMARK 3 L13: -0.2482 L23: 0.6424 REMARK 3 S TENSOR REMARK 3 S11: 0.0038 S12: 0.1490 S13: 0.0186 REMARK 3 S21: -0.0325 S22: -0.0548 S23: -0.0423 REMARK 3 S31: -0.1162 S32: 0.1632 S33: 0.0649 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 118:138) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3009 34.6489 -4.4123 REMARK 3 T TENSOR REMARK 3 T11: 0.1836 T22: 0.2365 REMARK 3 T33: 0.1795 T12: 0.0708 REMARK 3 T13: 0.0153 T23: 0.0169 REMARK 3 L TENSOR REMARK 3 L11: 2.7577 L22: 0.7096 REMARK 3 L33: 1.2012 L12: -0.8262 REMARK 3 L13: 0.3122 L23: 0.4908 REMARK 3 S TENSOR REMARK 3 S11: 0.4634 S12: 0.2953 S13: -0.0720 REMARK 3 S21: -0.1464 S22: -0.3111 S23: 0.1598 REMARK 3 S31: -0.1858 S32: -0.3181 S33: -0.1038 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 139:151) REMARK 3 ORIGIN FOR THE GROUP (A): -7.3568 26.4935 -3.8426 REMARK 3 T TENSOR REMARK 3 T11: 0.1305 T22: 0.1274 REMARK 3 T33: 0.0846 T12: -0.0176 REMARK 3 T13: 0.0066 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 0.2466 L22: 0.8801 REMARK 3 L33: 1.8736 L12: -0.0376 REMARK 3 L13: 0.2395 L23: -0.1431 REMARK 3 S TENSOR REMARK 3 S11: -0.0294 S12: 0.0382 S13: 0.1257 REMARK 3 S21: -0.0345 S22: -0.0186 S23: -0.0981 REMARK 3 S31: -0.3676 S32: -0.0402 S33: 0.0318 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 152:165) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1863 24.5599 -11.3339 REMARK 3 T TENSOR REMARK 3 T11: 0.1243 T22: 0.1502 REMARK 3 T33: 0.0818 T12: 0.0286 REMARK 3 T13: -0.0029 T23: 0.0202 REMARK 3 L TENSOR REMARK 3 L11: 0.1774 L22: 1.6271 REMARK 3 L33: 0.3156 L12: -0.2215 REMARK 3 L13: -0.1141 L23: -0.2707 REMARK 3 S TENSOR REMARK 3 S11: 0.1054 S12: 0.0784 S13: 0.1141 REMARK 3 S21: -0.1855 S22: -0.2508 S23: -0.0112 REMARK 3 S31: -0.0251 S32: 0.0800 S33: 0.1082 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 166:208) REMARK 3 ORIGIN FOR THE GROUP (A): -19.9033 14.8809 5.6810 REMARK 3 T TENSOR REMARK 3 T11: 0.0687 T22: 0.0762 REMARK 3 T33: 0.0860 T12: 0.0022 REMARK 3 T13: -0.0046 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.9127 L22: 0.6244 REMARK 3 L33: 0.7323 L12: 0.2792 REMARK 3 L13: 0.1013 L23: 0.3643 REMARK 3 S TENSOR REMARK 3 S11: -0.0536 S12: 0.0098 S13: -0.1106 REMARK 3 S21: 0.0386 S22: 0.0786 S23: -0.0661 REMARK 3 S31: 0.0474 S32: 0.0707 S33: -0.0455 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 209:238) REMARK 3 ORIGIN FOR THE GROUP (A): -17.0034 25.1392 4.0766 REMARK 3 T TENSOR REMARK 3 T11: 0.0890 T22: 0.1233 REMARK 3 T33: 0.0835 T12: -0.0239 REMARK 3 T13: -0.0120 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.0562 L22: 1.4892 REMARK 3 L33: 0.8670 L12: -0.7376 REMARK 3 L13: -0.3602 L23: -0.0978 REMARK 3 S TENSOR REMARK 3 S11: -0.0161 S12: 0.0827 S13: 0.1239 REMARK 3 S21: -0.0445 S22: 0.0051 S23: -0.2400 REMARK 3 S31: -0.1653 S32: 0.0702 S33: 0.0257 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 239:283) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7921 22.6065 6.5538 REMARK 3 T TENSOR REMARK 3 T11: 0.0909 T22: 0.0645 REMARK 3 T33: 0.1002 T12: 0.0053 REMARK 3 T13: -0.0225 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.8448 L22: 0.2345 REMARK 3 L33: 0.6407 L12: 0.0684 REMARK 3 L13: -0.0952 L23: -0.0341 REMARK 3 S TENSOR REMARK 3 S11: -0.0518 S12: -0.0193 S13: 0.1327 REMARK 3 S21: -0.0204 S22: 0.0149 S23: 0.1823 REMARK 3 S31: -0.1357 S32: 0.0414 S33: 0.0408 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: (CHAIN A AND RESID 284:325) REMARK 3 ORIGIN FOR THE GROUP (A): -35.1779 15.5200 11.3834 REMARK 3 T TENSOR REMARK 3 T11: 0.0895 T22: 0.0738 REMARK 3 T33: 0.1253 T12: -0.0088 REMARK 3 T13: 0.0267 T23: 0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.8385 L22: 1.0455 REMARK 3 L33: 0.8777 L12: -0.1800 REMARK 3 L13: 0.2514 L23: -0.1479 REMARK 3 S TENSOR REMARK 3 S11: -0.0333 S12: -0.1049 S13: -0.1236 REMARK 3 S21: 0.0976 S22: 0.0100 S23: 0.2432 REMARK 3 S31: 0.1060 S32: -0.0920 S33: 0.0156 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: (CHAIN A AND RESID 326:338) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5162 22.2326 21.2906 REMARK 3 T TENSOR REMARK 3 T11: 0.1817 T22: 0.1537 REMARK 3 T33: 0.0460 T12: 0.0111 REMARK 3 T13: -0.0528 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.5906 L22: 1.7423 REMARK 3 L33: 0.2723 L12: 0.3334 REMARK 3 L13: -0.1286 L23: -0.6438 REMARK 3 S TENSOR REMARK 3 S11: 0.1264 S12: -0.1155 S13: 0.0688 REMARK 3 S21: 0.4545 S22: -0.1383 S23: -0.0460 REMARK 3 S31: -0.2071 S32: 0.1377 S33: 0.0372 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: (CHAIN A AND RESID 339:357) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1227 8.9633 14.2790 REMARK 3 T TENSOR REMARK 3 T11: 0.1738 T22: 0.1675 REMARK 3 T33: 0.1966 T12: 0.0407 REMARK 3 T13: -0.0008 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 0.8660 L22: 0.8243 REMARK 3 L33: 2.1632 L12: 0.2832 REMARK 3 L13: -0.5420 L23: -0.1312 REMARK 3 S TENSOR REMARK 3 S11: -0.3661 S12: -0.0517 S13: -0.4256 REMARK 3 S21: 0.1317 S22: 0.0964 S23: -0.3349 REMARK 3 S31: 0.4486 S32: 0.2868 S33: 0.1476 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 4A07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1290049550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-09 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) : 0.9999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 47.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.72000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2 M NA CITRATE 0.1 M HEPES PH 7.5 10 REMARK 280 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 74.10500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.10500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.01500 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLN 288 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 292 TO GLY 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 N CA CB CG CD NE CZ REMARK 470 ARG A 75 NH1 NH2 REMARK 470 ARG A 78 CD NE CZ NH1 NH2 REMARK 470 LYS A 83 CE NZ REMARK 470 ARG A 100 CD NE CZ NH1 NH2 REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 LYS A 144 CE NZ REMARK 470 GLU A 153 CD OE1 OE2 REMARK 470 LYS A 163 CD CE NZ REMARK 470 ARG A 172 NE CZ NH1 NH2 REMARK 470 LYS A 173 CD CE NZ REMARK 470 LYS A 199 CE NZ REMARK 470 GLU A 215 CD OE1 OE2 REMARK 470 LYS A 235 CE NZ REMARK 470 ARG A 238 NE CZ NH1 NH2 REMARK 470 LYS A 257 NZ REMARK 470 LYS A 323 CE NZ REMARK 470 GLU A 343 CD OE1 OE2 REMARK 470 ASN A 349 CG OD1 ND2 REMARK 470 GLN A 352 CD OE1 NE2 REMARK 470 LYS A 357 CG CD CE NZ REMARK 470 THR A 359 C O CB OG1 CG2 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 HG1 THR A 180 HG SER A 231 1545 1.05 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 61.79 -150.58 REMARK 500 ASP A 151 -161.31 -125.31 REMARK 500 ARG A 204 -12.14 80.07 REMARK 500 ASP A 223 72.40 76.01 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 A2035 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A2040 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2110 DISTANCE = 6.11 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 PS171 (AZ7): ALLOSTERIC ACTIVATOR PS171 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 MG A 800 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 223 OD1 REMARK 620 2 ATP A 500 O1A 155.3 REMARK 620 3 ATP A 500 O2B 107.5 82.2 REMARK 620 N 1 2 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR PROVIDED. 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 AZ7 A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AZ7 A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 860 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 870 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 890 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1H1W RELATED DB: PDB REMARK 900 HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 CATALYTIC DOMAIN REMARK 900 RELATED ID: 1UU3 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531 REMARK 900 RELATED ID: 1W1G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND REMARK 900 TO DIC4-PHOSPHATIDYLINOSITOL (3,4,5)- TRISPHOSPHATE REMARK 900 RELATED ID: 1W1H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN REMARK 900 RELATED ID: 2BIY RELATED DB: PDB REMARK 900 STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN REMARK 900 RELATED ID: 1UU8 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1 REMARK 900 RELATED ID: 1OKY RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE REMARK 900 RELATED ID: 1UU9 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3 REMARK 900 RELATED ID: 1Z5M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N1-[3-[[5-BROMO-2-[[3-[(1- REMARK 900 PYRROLIDINYLCARBONYL)AMINO]PHENYL]AMINO]-4-PYRIMIDINYL] AMINO] REMARK 900 PROPYL]-2,2-DIMETHYLPROPANEDIAMIDECOMPLEXED WITH HUMAN PDK1 REMARK 900 RELATED ID: 1OKZ RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01 REMARK 900 RELATED ID: 1W1D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND REMARK 900 TO INOSITOL (1,3,4,5)-TETRAKISPHOSPHATE REMARK 900 RELATED ID: 2XCH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH A PYRAZOLOQUINAZOLINE REMARK 900 INHIBITOR REMARK 900 RELATED ID: 2VKI RELATED DB: PDB REMARK 900 STRUCTURE OF THE PDK1 PH DOMAIN K465E MUTANT REMARK 900 RELATED ID: 2XCK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH A PYRAZOLOQUINAZOLINE REMARK 900 INHIBITOR REMARK 900 RELATED ID: 1UU7 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-2 REMARK 900 RELATED ID: 1UVR RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8 REMARK 900 RELATED ID: 4A06 RELATED DB: PDB REMARK 900 HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC ACTIVATOR PS114 REMARK 900 BOUND TO THE PIF-POCKET DBREF 4A07 A 50 359 UNP O15530 PDPK1_HUMAN 50 359 SEQADV 4A07 GLY A 49 UNP O15530 EXPRESSION TAG SEQADV 4A07 GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 4A07 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 CSS 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 4A07 SEP A 241 SER PHOSPHOSERINE MODRES 4A07 CSS A 260 CYS S-MERCAPTOCYSTEINE HET SEP A 241 12 HET CSS A 260 7 HET ATP A 500 35 HET AZ7 A 600 24 HET AZ7 A 700 24 HET MG A 800 1 HET CL A 850 1 HET CL A 860 1 HET CL A 870 1 HET CL A 880 1 HET CL A 890 1 HETNAM SEP PHOSPHOSERINE HETNAM CSS S-MERCAPTOCYSTEINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM AZ7 (3S)-3-(4-CHLOROPHENYL)-4-(5,7-DICHLORO-1H- HETNAM 2 AZ7 BENZIMIDAZOL-2-YL)BUTANOIC ACID HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 1 CSS C3 H7 N O2 S2 FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 AZ7 2(C17 H13 CL3 N2 O2) FORMUL 5 MG MG 2+ FORMUL 6 CL 5(CL 1-) FORMUL 11 HOH *209(H2 O) HELIX 1 1 LYS A 115 GLU A 121 1 7 HELIX 2 2 LYS A 123 SER A 135 1 13 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 LEU A 159 -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 1.33 LINK C SEP A 241 N PHE A 242 1555 1555 1.33 LINK C ALA A 259 N CSS A 260 1555 1555 1.33 LINK C CSS A 260 N LYS A 261 1555 1555 1.33 LINK OD1 ASP A 223 MG MG A 800 1555 1555 2.21 LINK O1A ATP A 500 MG MG A 800 1555 1555 2.32 LINK O2B ATP A 500 MG MG A 800 1555 1555 2.28 SITE 1 AC1 18 GLY A 89 GLY A 91 SER A 92 SER A 94 SITE 2 AC1 18 VAL A 96 ALA A 109 LYS A 111 SER A 160 SITE 3 AC1 18 ALA A 162 GLU A 166 LEU A 212 ASP A 223 SITE 4 AC1 18 MG A 800 HOH A2019 HOH A2128 HOH A2131 SITE 5 AC1 18 HOH A2132 HOH A2209 SITE 1 AC2 9 LYS A 76 LYS A 115 ILE A 119 VAL A 124 SITE 2 AC2 9 ARG A 131 THR A 148 GLN A 150 LEU A 155 SITE 3 AC2 9 PHE A 157 SITE 1 AC3 11 LEU A 168 ARG A 172 PHE A 242 LEU A 253 SITE 2 AC3 11 LEU A 254 LYS A 257 GLN A 274 GLY A 278 SITE 3 AC3 11 PHE A 282 ARG A 283 PHE A 291 SITE 1 AC4 3 LYS A 111 ASP A 223 ATP A 500 SITE 1 AC5 1 ASP A 311 SITE 1 AC6 1 LEU A 350 SITE 1 AC7 2 LYS A 169 TYR A 170 CRYST1 148.210 44.030 47.670 90.00 101.23 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 0.001340 0.00000 SCALE2 0.000000 0.022712 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021387 0.00000