HEADER TRANSFERASE 30-MAY-12 4AW0 TITLE HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND PS182 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 51-359; 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_PLASMID: PFASTBAC KEYWDS TRANSFERASE, ALLOSTERIC REGULATION, ALLOSTERIC SITE, PHOSPHORYLATION, KEYWDS 2 AGC PROTEIN KINASE EXPDTA X-RAY DIFFRACTION AUTHOR J.O.SCHULZE,K.BUSSCHOTS,L.A.LOPEZ-GARCIA,C.LAMMI,A.STROBA,S.ZEUZEM, AUTHOR 2 A.PIIPER,P.M.ALZARI,S.NEIMANIS,J.M.ARENCIBIA,M.ENGEL,R.M.BIONDI REVDAT 3 20-DEC-23 4AW0 1 REMARK LINK ATOM REVDAT 2 10-OCT-12 4AW0 1 COMPND REMARK DBREF SEQADV REVDAT 2 2 1 HELIX SHEET MASTER REVDAT 1 03-OCT-12 4AW0 0 JRNL AUTH K.BUSSCHOTS,L.A.LOPEZ-GARCIA,C.LAMMI,A.STROBA,S.ZEUZEM, JRNL AUTH 2 A.PIIPER,P.M.ALZARI,S.NEIMANIS,J.M.ARENCIBIA,M.ENGEL, JRNL AUTH 3 J.O.SCHULZE,R.M.BIONDI JRNL TITL SUBSTRATE-SELECTIVE INHIBITION OF PROTEIN KINASE PDK1 BY JRNL TITL 2 SMALL COMPOUNDS THAT BIND TO THE PIF-POCKET ALLOSTERIC JRNL TITL 3 DOCKING SITE. JRNL REF CHEM.BIOL. V. 19 1152 2012 JRNL REFN ISSN 1074-5521 JRNL PMID 22999883 JRNL DOI 10.1016/J.CHEMBIOL.2012.07.017 REMARK 2 REMARK 2 RESOLUTION. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 53019 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2651 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 46.4519 - 3.8148 0.92 2647 139 0.1710 0.1736 REMARK 3 2 3.8148 - 3.0281 0.94 2673 141 0.1547 0.1656 REMARK 3 3 3.0281 - 2.6454 0.96 2668 140 0.1646 0.1749 REMARK 3 4 2.6454 - 2.4035 0.98 2736 144 0.1643 0.2012 REMARK 3 5 2.4035 - 2.2312 0.94 2604 137 0.1535 0.1741 REMARK 3 6 2.2312 - 2.0997 0.96 2687 141 0.1498 0.1844 REMARK 3 7 2.0997 - 1.9945 0.92 2558 135 0.1517 0.1697 REMARK 3 8 1.9945 - 1.9077 0.93 2553 134 0.1615 0.1832 REMARK 3 9 1.9077 - 1.8343 0.95 2636 139 0.1690 0.2156 REMARK 3 10 1.8343 - 1.7710 0.98 2741 145 0.1723 0.1826 REMARK 3 11 1.7710 - 1.7156 0.98 2706 142 0.1738 0.2048 REMARK 3 12 1.7156 - 1.6666 0.98 2690 142 0.1801 0.2321 REMARK 3 13 1.6666 - 1.6227 0.98 2698 142 0.1861 0.2413 REMARK 3 14 1.6227 - 1.5831 0.98 2678 140 0.1931 0.1961 REMARK 3 15 1.5831 - 1.5471 0.97 2722 144 0.2025 0.2336 REMARK 3 16 1.5471 - 1.5142 0.92 2520 132 0.2260 0.2295 REMARK 3 17 1.5142 - 1.4839 0.97 2692 142 0.2371 0.2440 REMARK 3 18 1.4839 - 1.4559 0.94 2585 136 0.2610 0.2727 REMARK 3 19 1.4559 - 1.4299 0.94 2574 136 0.2841 0.2908 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 : 0.73 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 47.28 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.30380 REMARK 3 B22 (A**2) : 1.67580 REMARK 3 B33 (A**2) : -1.37200 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.07530 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 : 0.014 2660 REMARK 3 ANGLE : 1.445 3653 REMARK 3 CHIRALITY : 0.088 406 REMARK 3 PLANARITY : 0.008 464 REMARK 3 DIHEDRAL : 15.352 1027 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 75:150) REMARK 3 ORIGIN FOR THE GROUP (A): -10.2136 27.5305 -9.7869 REMARK 3 T TENSOR REMARK 3 T11: 0.1365 T22: 0.2599 REMARK 3 T33: 0.1780 T12: 0.0587 REMARK 3 T13: 0.0266 T23: 0.0407 REMARK 3 L TENSOR REMARK 3 L11: 0.5767 L22: 1.1497 REMARK 3 L33: 2.2027 L12: 0.0756 REMARK 3 L13: -0.5508 L23: 0.1448 REMARK 3 S TENSOR REMARK 3 S11: 0.2424 S12: 0.2115 S13: 0.2311 REMARK 3 S21: -0.0863 S22: -0.0892 S23: 0.1388 REMARK 3 S31: -0.4271 S32: -0.2148 S33: -0.0628 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 151:277) REMARK 3 ORIGIN FOR THE GROUP (A): -21.2918 20.8477 3.4334 REMARK 3 T TENSOR REMARK 3 T11: 0.0783 T22: 0.0660 REMARK 3 T33: 0.0678 T12: -0.0030 REMARK 3 T13: -0.0123 T23: -0.0103 REMARK 3 L TENSOR REMARK 3 L11: 1.6894 L22: 1.3536 REMARK 3 L33: 1.2622 L12: 0.0940 REMARK 3 L13: -0.2324 L23: -0.4343 REMARK 3 S TENSOR REMARK 3 S11: 0.0289 S12: 0.0621 S13: 0.1236 REMARK 3 S21: -0.0823 S22: -0.0026 S23: 0.0396 REMARK 3 S31: -0.0544 S32: 0.0943 S33: 0.0001 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 278:327) REMARK 3 ORIGIN FOR THE GROUP (A): -35.1096 15.8739 10.4839 REMARK 3 T TENSOR REMARK 3 T11: 0.1230 T22: 0.0865 REMARK 3 T33: 0.1657 T12: -0.0061 REMARK 3 T13: 0.0000 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.6773 L22: 1.6449 REMARK 3 L33: 1.2280 L12: -0.2048 REMARK 3 L13: 0.2170 L23: -0.2989 REMARK 3 S TENSOR REMARK 3 S11: 0.0335 S12: -0.1803 S13: -0.0765 REMARK 3 S21: -0.0133 S22: 0.0195 S23: 0.3450 REMARK 3 S31: 0.0790 S32: -0.0930 S33: -0.0598 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 328:359) REMARK 3 ORIGIN FOR THE GROUP (A): -15.8579 14.4705 16.6318 REMARK 3 T TENSOR REMARK 3 T11: 0.1425 T22: 0.1867 REMARK 3 T33: 0.1085 T12: 0.0326 REMARK 3 T13: -0.0396 T23: 0.0168 REMARK 3 L TENSOR REMARK 3 L11: 2.5769 L22: 1.6305 REMARK 3 L33: 1.7815 L12: -0.1545 REMARK 3 L13: -0.5614 L23: 0.0804 REMARK 3 S TENSOR REMARK 3 S11: -0.0368 S12: -0.2261 S13: -0.2240 REMARK 3 S21: 0.1618 S22: 0.0360 S23: -0.1731 REMARK 3 S31: 0.1832 S32: 0.2643 S33: -0.0027 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 4AW0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1290052708. 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 : SI-111 CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53029 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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, 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 74.13500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.00500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.13500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.00500 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 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, TYR 238 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLN 242 TO ALA 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 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 78 NE CZ NH1 NH2 REMARK 470 LYS A 83 CE NZ REMARK 470 LYS A 86 NZ 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 LYS A 154 NZ REMARK 470 LYS A 163 CE NZ REMARK 470 ARG A 172 CD NE CZ NH1 NH2 REMARK 470 LYS A 173 CD CE NZ REMARK 470 LYS A 199 CE NZ REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 ARG A 238 NE CZ NH1 NH2 REMARK 470 LYS A 257 CE NZ REMARK 470 CME A 260 CE CZ OH REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 304 CG CD CE NZ REMARK 470 LYS A 323 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 O GLY A 244 O HOH A 2155 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 HG1 THR A 180 HG SER A 231 1545 1.04 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 79.32 -163.01 REMARK 500 ASP A 138 45.12 -155.04 REMARK 500 ASP A 151 -159.12 -139.63 REMARK 500 ARG A 204 -12.94 79.45 REMARK 500 ASP A 223 76.19 78.73 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 A2107 DISTANCE = 6.10 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 MG A 850 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 210 OD1 REMARK 620 2 ASP A 223 OD2 96.0 REMARK 620 3 ATP A 500 O2B 161.6 66.2 REMARK 620 N 1 2 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 ASP A 223 OD2 48.5 REMARK 620 3 ATP A 500 O2B 111.9 70.9 REMARK 620 4 ATP A 500 O2A 136.5 118.5 94.8 REMARK 620 N 1 2 3 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 MJF A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS 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 MG A 850 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DTD A 900 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: 1OKY RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE 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: 1UU3 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531 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: 1UU8 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1 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: 1UVR RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8 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: 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: 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: 2BIY RELATED DB: PDB REMARK 900 STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN REMARK 900 RELATED ID: 2VKI RELATED DB: PDB REMARK 900 STRUCTURE OF THE PDK1 PH DOMAIN K465E MUTANT 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: 2XCK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH A PYRAZOLOQUINAZOLINE REMARK 900 INHIBITOR 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 REMARK 900 RELATED ID: 4A07 RELATED DB: PDB REMARK 900 HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC ACTIVATOR PS171 REMARK 900 BOUND TO THE PIF-POCKET REMARK 900 RELATED ID: 4AW1 RELATED DB: PDB REMARK 900 HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND PS210 REMARK 900 BOUND TO THE PIF-POCKET DBREF 4AW0 A 51 359 UNP O15530 PDPK1_HUMAN 51 359 SEQADV 4AW0 GLY A 49 UNP O15530 EXPRESSION TAG SEQADV 4AW0 ALA A 50 UNP O15530 EXPRESSION TAG SEQADV 4AW0 GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 4AW0 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 CME 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 4AW0 SEP A 241 SER PHOSPHOSERINE MODRES 4AW0 CME A 260 CYS S,S-(2-HYDROXYETHYL)THIOCYSTEINE HET SEP A 241 14 HET CME A 260 7 HET ATP A 500 35 HET MJF A 600 24 HET DMS A 700 4 HET MG A 800 1 HET MG A 850 1 HET DTD A 900 8 HETNAM SEP PHOSPHOSERINE HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MJF [(1R)-3-(4-CHLOROPHENYL)-3-OXO-1- HETNAM 2 MJF PHENYLPROPYL]PROPANEDIOIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM MG MAGNESIUM ION HETNAM DTD DITHIANE DIOL HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 1 CME C5 H11 N O3 S2 FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 MJF C18 H15 CL O5 FORMUL 4 DMS C2 H6 O S FORMUL 5 MG 2(MG 2+) FORMUL 7 DTD C4 H8 O2 S2 FORMUL 8 HOH *227(H2 O) HELIX 1 1 LYS A 115 GLU A 121 1 7 HELIX 2 2 PRO A 125 SER A 135 1 11 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 1.32 LINK C SEP A 241 N PHE A 242 1555 1555 1.32 LINK C ALA A 259 N CME A 260 1555 1555 1.32 LINK C CME A 260 N LYS A 261 1555 1555 1.33 LINK OD1 ASN A 210 MG MG A 850 1555 1555 2.31 LINK OD1BASP A 223 MG MG A 800 1555 1555 2.70 LINK OD2AASP A 223 MG MG A 800 1555 1555 2.21 LINK OD2AASP A 223 MG MG A 850 1555 1555 2.11 LINK O2B ATP A 500 MG MG A 800 1555 1555 2.08 LINK O2A ATP A 500 MG MG A 800 1555 1555 2.32 LINK O2B ATP A 500 MG MG A 850 1555 1555 2.42 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 ASP A 223 SITE 4 AC1 22 MG A 800 MG A 850 HOH A2017 HOH A2019 SITE 5 AC1 22 HOH A2020 HOH A2021 HOH A2136 HOH A2137 SITE 6 AC1 22 HOH A2138 HOH A2232 SITE 1 AC2 10 LYS A 76 VAL A 127 THR A 128 ARG A 131 SITE 2 AC2 10 THR A 148 PHE A 149 GLN A 150 LEU A 155 SITE 3 AC2 10 TYR A 156 HOH A2072 SITE 1 AC3 9 THR A 104 SER A 105 HIS A 139 SER A 191 SITE 2 AC3 9 TRP A 347 GLU A 348 ASN A 349 LEU A 350 SITE 3 AC3 9 HIS A 351 SITE 1 AC4 4 LYS A 111 ASP A 223 ATP A 500 MG A 850 SITE 1 AC5 5 ASN A 210 ASP A 223 ATP A 500 MG A 800 SITE 2 AC5 5 HOH A2130 SITE 1 AC6 8 PHE A 242 VAL A 243 GLY A 244 ALA A 246 SITE 2 AC6 8 VAL A 249 ARG A 283 GLU A 287 HOH A2177 CRYST1 148.270 44.010 47.390 90.00 101.57 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 0.006744 0.000000 0.001381 0.00000 SCALE2 0.000000 0.022722 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021539 0.00000