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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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