HEADER TRANSFERASE 30-MAY-12 4AW1 TITLE HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND PS210 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; COMPND 9 OTHER_DETAILS: PHOSPHORYLATION AT S241 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 4 20-NOV-24 4AW1 1 REMARK REVDAT 3 20-DEC-23 4AW1 1 REMARK LINK ATOM REVDAT 2 10-OCT-12 4AW1 1 COMPND REMARK DBREF SEQADV REVDAT 2 2 1 HELIX SHEET MASTER REVDAT 1 03-OCT-12 4AW1 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. 1.68 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) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 32317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1617 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 36.3099 - 3.8447 0.99 2640 139 0.1666 0.1612 REMARK 3 2 3.8447 - 3.0521 1.00 2583 136 0.1489 0.1690 REMARK 3 3 3.0521 - 2.6664 1.00 2568 136 0.1549 0.1811 REMARK 3 4 2.6664 - 2.4227 1.00 2540 133 0.1570 0.2108 REMARK 3 5 2.4227 - 2.2491 1.00 2559 135 0.1475 0.1942 REMARK 3 6 2.2491 - 2.1165 1.00 2550 134 0.1429 0.1761 REMARK 3 7 2.1165 - 2.0105 1.00 2556 135 0.1514 0.1621 REMARK 3 8 2.0105 - 1.9230 1.00 2546 134 0.1665 0.2301 REMARK 3 9 1.9230 - 1.8490 1.00 2523 133 0.1927 0.2181 REMARK 3 10 1.8490 - 1.7852 1.00 2555 134 0.2069 0.2205 REMARK 3 11 1.7852 - 1.7294 1.00 2526 133 0.2281 0.2388 REMARK 3 12 1.7294 - 1.6799 1.00 2554 135 0.2683 0.3126 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 48.85 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.40790 REMARK 3 B22 (A**2) : -1.10750 REMARK 3 B33 (A**2) : -1.30040 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -6.57370 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 : 0.007 2407 REMARK 3 ANGLE : 1.223 3282 REMARK 3 CHIRALITY : 0.072 365 REMARK 3 PLANARITY : 0.006 413 REMARK 3 DIHEDRAL : 13.691 880 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 66:94) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8031 29.3081 -10.4603 REMARK 3 T TENSOR REMARK 3 T11: 0.2151 T22: 0.2565 REMARK 3 T33: 0.3111 T12: 0.0193 REMARK 3 T13: 0.0122 T23: -0.0426 REMARK 3 L TENSOR REMARK 3 L11: 0.9813 L22: 1.4107 REMARK 3 L33: 3.0734 L12: -0.1183 REMARK 3 L13: 0.1906 L23: -0.0642 REMARK 3 S TENSOR REMARK 3 S11: -0.0635 S12: 0.0280 S13: 0.6863 REMARK 3 S21: 0.1200 S22: 0.0312 S23: 0.1272 REMARK 3 S31: -0.3967 S32: 0.1108 S33: 0.1235 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 95:120) REMARK 3 ORIGIN FOR THE GROUP (A): -9.3476 25.2602 -13.8351 REMARK 3 T TENSOR REMARK 3 T11: 0.1221 T22: 0.2293 REMARK 3 T33: 0.0697 T12: 0.0139 REMARK 3 T13: 0.0016 T23: 0.0325 REMARK 3 L TENSOR REMARK 3 L11: 3.1321 L22: 5.1424 REMARK 3 L33: 2.1043 L12: -1.5674 REMARK 3 L13: -1.0321 L23: 0.6297 REMARK 3 S TENSOR REMARK 3 S11: 0.1188 S12: 0.2348 S13: -0.1242 REMARK 3 S21: -0.1327 S22: -0.0684 S23: 0.2430 REMARK 3 S31: -0.1036 S32: -0.1888 S33: -0.0550 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 121:178) REMARK 3 ORIGIN FOR THE GROUP (A): -13.7862 24.2033 -4.2346 REMARK 3 T TENSOR REMARK 3 T11: 0.1108 T22: 0.1969 REMARK 3 T33: 0.1550 T12: 0.0211 REMARK 3 T13: 0.0007 T23: -0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.9973 L22: 2.6033 REMARK 3 L33: 2.5197 L12: 0.8846 REMARK 3 L13: -0.8310 L23: -1.4525 REMARK 3 S TENSOR REMARK 3 S11: 0.0329 S12: 0.0118 S13: 0.0832 REMARK 3 S21: 0.0121 S22: -0.0392 S23: 0.0619 REMARK 3 S31: -0.2176 S32: -0.0422 S33: 0.0192 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 179:198) REMARK 3 ORIGIN FOR THE GROUP (A): -16.2457 14.0380 10.8132 REMARK 3 T TENSOR REMARK 3 T11: 0.0889 T22: 0.1519 REMARK 3 T33: 0.0891 T12: 0.0163 REMARK 3 T13: 0.0043 T23: 0.0167 REMARK 3 L TENSOR REMARK 3 L11: 3.4496 L22: 4.4985 REMARK 3 L33: 2.7196 L12: 0.2801 REMARK 3 L13: 0.1614 L23: 0.8780 REMARK 3 S TENSOR REMARK 3 S11: -0.0324 S12: -0.1396 S13: -0.1847 REMARK 3 S21: 0.1129 S22: -0.0382 S23: -0.1930 REMARK 3 S31: 0.2365 S32: 0.0782 S33: 0.0962 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 199:277) REMARK 3 ORIGIN FOR THE GROUP (A): -23.7049 22.7752 4.9111 REMARK 3 T TENSOR REMARK 3 T11: 0.0901 T22: 0.1078 REMARK 3 T33: 0.1050 T12: -0.0018 REMARK 3 T13: -0.0248 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 2.6908 L22: 2.1836 REMARK 3 L33: 1.7319 L12: 0.1333 REMARK 3 L13: -0.2239 L23: -0.0667 REMARK 3 S TENSOR REMARK 3 S11: -0.0751 S12: 0.0907 S13: 0.2741 REMARK 3 S21: -0.0325 S22: 0.0124 S23: 0.2126 REMARK 3 S31: -0.1811 S32: -0.1030 S33: 0.0391 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 278:337) REMARK 3 ORIGIN FOR THE GROUP (A): -31.9210 15.9739 12.6625 REMARK 3 T TENSOR REMARK 3 T11: 0.1094 T22: 0.1859 REMARK 3 T33: 0.1753 T12: -0.0175 REMARK 3 T13: 0.0554 T23: -0.0051 REMARK 3 L TENSOR REMARK 3 L11: 2.3007 L22: 1.4037 REMARK 3 L33: 2.1658 L12: -0.4541 REMARK 3 L13: 1.5518 L23: 0.0169 REMARK 3 S TENSOR REMARK 3 S11: -0.0494 S12: -0.2176 S13: -0.1048 REMARK 3 S21: 0.1316 S22: -0.0328 S23: 0.3787 REMARK 3 S31: 0.1173 S32: -0.2592 S33: 0.0297 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN A AND (RESSEQ 338:359) REMARK 3 ORIGIN FOR THE GROUP (A): -12.6878 7.9841 13.5599 REMARK 3 T TENSOR REMARK 3 T11: 0.1777 T22: 0.1839 REMARK 3 T33: 0.1814 T12: 0.0546 REMARK 3 T13: -0.0535 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 5.4422 L22: 3.8102 REMARK 3 L33: 4.6852 L12: -1.7921 REMARK 3 L13: -4.6456 L23: 1.1249 REMARK 3 S TENSOR REMARK 3 S11: -0.0301 S12: -0.3107 S13: -0.3491 REMARK 3 S21: 0.2270 S22: -0.0172 S23: -0.2841 REMARK 3 S31: 0.2234 S32: 0.3958 S33: -0.0027 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 72-74 ARE DISORDERED REMARK 4 REMARK 4 4AW1 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_1290052698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : 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 : 32322 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 36.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 72.82500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.33500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.82500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.33500 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 73 REMARK 465 PRO A 74 REMARK 465 PRO A 232 REMARK 465 GLU A 233 REMARK 465 SER A 234 REMARK 465 LYS A 235 REMARK 465 GLN A 236 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 PRO A 72 CA C O CB CG CD REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 LYS A 86 CE NZ REMARK 470 ARG A 116 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 120 CD CE NZ REMARK 470 LYS A 144 CE NZ REMARK 470 ASP A 152 CG OD1 OD2 REMARK 470 GLU A 153 CD OE1 OE2 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 GLU A 215 CD OE1 OE2 REMARK 470 SER A 231 CA C O CB OG REMARK 470 ALA A 237 N CB REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 257 CD CE NZ REMARK 470 ARG A 283 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 304 CE NZ REMARK 470 LYS A 323 CE NZ REMARK 470 GLU A 328 CD OE1 OE2 REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 GLU A 348 CG CD OE1 OE2 REMARK 470 LYS A 357 CD CE NZ REMARK 470 THR A 359 CA C O CB OG1 CG2 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 SER A 105 12.62 58.73 REMARK 500 ASP A 138 49.92 -146.02 REMARK 500 ARG A 204 -13.29 78.32 REMARK 500 ASP A 223 84.69 68.96 REMARK 500 LYS A 304 49.17 -101.28 REMARK 500 REMARK 500 REMARK: NULL 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 NA A1366 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 191 O REMARK 620 2 GLU A 194 OE1 108.2 REMARK 620 3 HOH A2025 O 115.1 100.2 REMARK 620 4 HOH A2044 O 101.3 139.5 91.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1365 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 210 OD1 REMARK 620 2 ASP A 223 OD2 93.2 REMARK 620 3 ATP A1360 O1G 151.7 72.6 REMARK 620 4 ATP A1360 O3B 161.0 99.2 47.1 REMARK 620 5 ATP A1360 O1A 84.9 106.8 122.2 77.8 REMARK 620 6 HOH A2088 O 101.2 84.6 54.3 94.3 166.9 REMARK 620 7 HOH A2090 O 48.5 128.9 156.4 112.9 48.4 128.7 REMARK 620 8 HOH A2091 O 78.1 170.4 113.5 90.3 76.7 93.0 46.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1364 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 223 OD2 REMARK 620 2 ASP A 223 OD1 54.7 REMARK 620 3 ATP A1360 O1B 89.5 80.9 REMARK 620 4 ATP A1360 O1G 87.0 140.0 88.4 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 1360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 21O A 1361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1364 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1365 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1366 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1369 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: 4AW0 RELATED DB: PDB REMARK 900 HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND PS182 REMARK 900 BOUND TO THE PIF-POCKET DBREF 4AW1 A 51 359 UNP O15530 PDPK1_HUMAN 51 359 SEQADV 4AW1 GLY A 49 UNP O15530 EXPRESSION TAG SEQADV 4AW1 ALA A 50 UNP O15530 EXPRESSION TAG SEQADV 4AW1 GLY A 288 UNP O15530 TYR 288 ENGINEERED MUTATION SEQADV 4AW1 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 4AW1 SEP A 241 SER PHOSPHOSERINE HET SEP A 241 12 HET ATP A1360 35 HET 21O A1361 27 HET DMS A1362 4 HET DMS A1363 4 HET MN A1364 1 HET NA A1365 1 HET NA A1366 1 HET CL A1367 1 HET CL A1368 1 HET CL A1369 1 HETNAM SEP PHOSPHOSERINE HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM 21O {(1R)-3-OXO-1-PHENYL-3-[4-(TRIFLUOROMETHYL) HETNAM 2 21O PHENYL]PROPYL}PROPANEDIOIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION HETSYN SEP PHOSPHONOSERINE FORMUL 1 SEP C3 H8 N O6 P FORMUL 2 ATP C10 H16 N5 O13 P3 FORMUL 3 21O C19 H15 F3 O5 FORMUL 4 DMS 2(C2 H6 O S) FORMUL 6 MN MN 2+ FORMUL 7 NA 2(NA 1+) FORMUL 9 CL 3(CL 1-) FORMUL 12 HOH *145(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 AA 5 PHE A 82 GLY A 91 0 SHEET 2 AA 5 SER A 94 GLU A 101 -1 O LEU A 98 N GLY A 85 SHEET 3 AA 5 ARG A 106 GLU A 114 -1 O ILE A 110 N VAL A 97 SHEET 4 AA 5 LYS A 154 SER A 160 -1 O LEU A 159 N ALA A 109 SHEET 5 AA 5 PHE A 147 ASP A 151 -1 N PHE A 147 O GLY A 158 SHEET 1 AB 3 GLY A 165 GLU A 166 0 SHEET 2 AB 3 ILE A 211 ASN A 214 -1 O LEU A 213 N GLY A 165 SHEET 3 AB 3 HIS A 218 ILE A 221 -1 O GLN A 220 N LEU A 212 SHEET 1 AC 2 ILE A 201 ILE A 202 0 SHEET 2 AC 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 O SER A 191 NA NA A1366 1555 1555 2.75 LINK OE1 GLU A 194 NA NA A1366 1555 1555 2.86 LINK OD1 ASN A 210 NA NA A1365 1555 1555 2.60 LINK OD2 ASP A 223 MN MN A1364 1555 1555 2.39 LINK OD1 ASP A 223 MN MN A1364 1555 1555 2.40 LINK OD2 ASP A 223 NA NA A1365 1555 1555 2.48 LINK O1B ATP A1360 MN MN A1364 1555 1555 2.13 LINK O1G ATP A1360 MN MN A1364 1555 1555 2.53 LINK O1G ATP A1360 NA NA A1365 1555 1555 3.17 LINK O3B ATP A1360 NA NA A1365 1555 1555 3.02 LINK O1A ATP A1360 NA NA A1365 1555 1555 2.52 LINK NA NA A1365 O HOH A2088 1555 1555 2.96 LINK NA NA A1365 O HOH A2090 1555 1555 3.15 LINK NA NA A1365 O HOH A2091 1555 1555 2.73 LINK NA NA A1366 O HOH A2025 1555 2555 2.87 LINK NA NA A1366 O HOH A2044 1555 1555 2.72 SITE 1 AC1 23 LEU A 88 GLY A 89 GLY A 91 SER A 92 SITE 2 AC1 23 SER A 94 VAL A 96 ALA A 109 LYS A 111 SITE 3 AC1 23 SER A 160 ALA A 162 GLU A 166 GLU A 209 SITE 4 AC1 23 ASN A 210 LEU A 212 ASP A 223 MN A1364 SITE 5 AC1 23 NA A1365 HOH A2012 HOH A2013 HOH A2017 SITE 6 AC1 23 HOH A2088 HOH A2090 HOH A2094 SITE 1 AC2 17 GLN A 66 HIS A 67 ALA A 68 LYS A 76 SITE 2 AC2 17 LYS A 115 ILE A 119 VAL A 124 VAL A 127 SITE 3 AC2 17 THR A 128 ARG A 131 THR A 148 PHE A 149 SITE 4 AC2 17 GLN A 150 LEU A 155 PHE A 157 HOH A2001 SITE 5 AC2 17 HOH A2051 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 A2077 SITE 1 AC4 3 ARG A 172 GLY A 278 ALA A 292 SITE 1 AC5 2 ASP A 223 ATP A1360 SITE 1 AC6 5 ASN A 210 ASP A 223 ATP A1360 HOH A2088 SITE 2 AC6 5 HOH A2091 SITE 1 AC7 4 SER A 191 GLU A 194 HOH A2025 HOH A2044 SITE 1 AC8 1 GLN A 247 CRYST1 145.650 42.670 46.330 90.00 98.52 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 0.006866 0.000000 0.001029 0.00000 SCALE2 0.000000 0.023436 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021825 0.00000