HEADER TRANSFERASE 19-DEC-07 2VKI TITLE STRUCTURE OF THE PDK1 PH DOMAIN K465E MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-PHOPSHOINOSITIDE DEPENDENT PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PLECKSTRIN HOMOLOGY (PH) DOMAIN, RESIDUES 409-556; 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P1 KEYWDS PLECKSTRIN HOMOLOGY, TRANSFERASE, CANCER, DIABETES EXPDTA X-RAY DIFFRACTION AUTHOR D.KOMANDER,J.R.BAYASCAS,M.DEAK,D.R.ALESSI,D.M.F.VAN AALTEN REVDAT 4 13-DEC-23 2VKI 1 REMARK REVDAT 3 13-JUL-11 2VKI 1 VERSN REVDAT 2 24-FEB-09 2VKI 1 VERSN REVDAT 1 13-MAY-08 2VKI 0 JRNL AUTH J.R.BAYASCAS,S.WULLSCHLEGER,K.SAKAMOTO,J.M.GARCIA-MARTINEZ, JRNL AUTH 2 C.CLACHER,D.KOMANDER,D.M.F.VAN AALTEN,K.M.BOINI,F.LANG, JRNL AUTH 3 C.LIPINA,L.LOGIE,C.SUTHERLAND,J.A.CHUDEK,J.A.VAN DIEPEN, JRNL AUTH 4 P.J.VOSHOL,J.M.LUCOCQ,D.R.ALESSI JRNL TITL MUTATION OF THE PDK1 PH DOMAIN INHIBITS PROTEIN KINASE JRNL TITL 2 B/AKT, LEADING TO SMALL SIZE AND INSULIN RESISTANCE. JRNL REF MOL.CELL.BIOL. V. 28 3258 2008 JRNL REFN ISSN 0270-7306 JRNL PMID 18347057 JRNL DOI 10.1128/MCB.02032-07 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 14309 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 609 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1000 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.3480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : -0.64000 REMARK 3 B33 (A**2) : 0.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.765 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1242 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1101 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1677 ; 1.681 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2566 ; 0.904 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 138 ; 7.298 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 170 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1354 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 271 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 215 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1257 ; 0.253 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 730 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 89 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 17 ; 0.190 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 79 ; 0.312 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.117 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 700 ; 0.983 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1137 ; 1.780 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 542 ; 2.542 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 540 ; 4.059 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 414 A 466 REMARK 3 RESIDUE RANGE : A 472 A 487 REMARK 3 RESIDUE RANGE : A 494 A 543 REMARK 3 ORIGIN FOR THE GROUP (A): 1.9703 17.6963 11.1860 REMARK 3 T TENSOR REMARK 3 T11: 0.0395 T22: 0.0345 REMARK 3 T33: 0.0428 T12: -0.0056 REMARK 3 T13: -0.0072 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 0.3314 L22: 1.1483 REMARK 3 L33: 0.8004 L12: -0.1515 REMARK 3 L13: 0.1228 L23: -0.1352 REMARK 3 S TENSOR REMARK 3 S11: -0.0030 S12: -0.0485 S13: -0.0011 REMARK 3 S21: 0.0306 S22: 0.0445 S23: -0.0373 REMARK 3 S31: -0.0251 S32: 0.0218 S33: -0.0415 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 410 A 413 REMARK 3 RESIDUE RANGE : A 467 A 471 REMARK 3 RESIDUE RANGE : A 544 A 549 REMARK 3 RESIDUE RANGE : A 488 A 493 REMARK 3 ORIGIN FOR THE GROUP (A): -0.7469 16.3049 12.3078 REMARK 3 T TENSOR REMARK 3 T11: 0.0117 T22: 0.0128 REMARK 3 T33: 0.0388 T12: 0.0080 REMARK 3 T13: -0.0076 T23: -0.0209 REMARK 3 L TENSOR REMARK 3 L11: 0.5356 L22: 0.2234 REMARK 3 L33: 1.0095 L12: -0.2601 REMARK 3 L13: 0.1261 L23: -0.0010 REMARK 3 S TENSOR REMARK 3 S11: -0.0394 S12: -0.0679 S13: 0.0286 REMARK 3 S21: 0.0022 S22: 0.0407 S23: 0.0228 REMARK 3 S31: 0.0028 S32: -0.0211 S33: -0.0013 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. DISORDERED RESIDUES WERE MODELLED AS ALA OR WITH OCCU REMARK 3 0.01. THE C-TERMINUS IS DISORDERED. REMARK 4 REMARK 4 2VKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1290034836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU IMAGE PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14950 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1W1D REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULPHATE, 0.1 M TRIS REMARK 280 HYDROCHLORIDE [PH 8.5] 30 % (W/V) PEG 4000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.00450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.90100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.52850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.90100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.00450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.52850 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, LYS 465 TO GLU 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 409 REMARK 465 HIS A 550 REMARK 465 PRO A 551 REMARK 465 ASP A 552 REMARK 465 ALA A 553 REMARK 465 ALA A 554 REMARK 465 VAL A 555 REMARK 465 GLN A 556 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 GLN A 429 CG CD OE1 NE2 REMARK 470 GLN A 548 CG CD OE1 NE2 REMARK 470 SER A 549 CA C O CB OG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 464 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 472 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES 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 GLN A 429 52.95 -99.73 REMARK 500 GLU A 480 143.53 -39.20 REMARK 500 GLN A 548 -70.98 121.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1549 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1550 REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 1UU9 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3 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: 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: 2BIY RELATED DB: PDB REMARK 900 STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN REMARK 900 RELATED ID: 1W1H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN 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 999 REMARK 999 SEQUENCE REMARK 999 POINT MUTATION K465E DBREF 2VKI A 409 556 UNP O15530 PDPK1_HUMAN 409 556 SEQADV 2VKI GLU A 465 UNP O15530 LYS 465 ENGINEERED MUTATION SEQRES 1 A 148 GLY SER ASN ILE GLU GLN TYR ILE HIS ASP LEU ASP SER SEQRES 2 A 148 ASN SER PHE GLU LEU ASP LEU GLN PHE SER GLU ASP GLU SEQRES 3 A 148 LYS ARG LEU LEU LEU GLU LYS GLN ALA GLY GLY ASN PRO SEQRES 4 A 148 TRP HIS GLN PHE VAL GLU ASN ASN LEU ILE LEU LYS MET SEQRES 5 A 148 GLY PRO VAL ASP GLU ARG LYS GLY LEU PHE ALA ARG ARG SEQRES 6 A 148 ARG GLN LEU LEU LEU THR GLU GLY PRO HIS LEU TYR TYR SEQRES 7 A 148 VAL ASP PRO VAL ASN LYS VAL LEU LYS GLY GLU ILE PRO SEQRES 8 A 148 TRP SER GLN GLU LEU ARG PRO GLU ALA LYS ASN PHE LYS SEQRES 9 A 148 THR PHE PHE VAL HIS THR PRO ASN ARG THR TYR TYR LEU SEQRES 10 A 148 MET ASP PRO SER GLY ASN ALA HIS LYS TRP CYS ARG LYS SEQRES 11 A 148 ILE GLN GLU VAL TRP ARG GLN ARG TYR GLN SER HIS PRO SEQRES 12 A 148 ASP ALA ALA VAL GLN HET GOL A1549 6 HET SO4 A1550 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *112(H2 O) HELIX 1 1 ASN A 411 GLN A 414 5 4 HELIX 2 2 SER A 431 ASN A 446 1 16 HELIX 3 3 TRP A 448 VAL A 452 5 5 HELIX 4 4 ASN A 531 GLN A 548 1 18 SHEET 1 AA 6 ILE A 416 ASP A 420 0 SHEET 2 AA 6 SER A 423 LEU A 426 -1 O SER A 423 N LEU A 419 SHEET 3 AA 6 ILE A 457 GLU A 465 -1 O LEU A 458 N LEU A 426 SHEET 4 AA 6 ARG A 472 THR A 479 -1 O ARG A 472 N GLU A 465 SHEET 5 AA 6 HIS A 483 ASP A 488 -1 O HIS A 483 N THR A 479 SHEET 6 AA 6 VAL A 493 ILE A 498 -1 O VAL A 493 N ASP A 488 SHEET 1 AB 6 ILE A 416 ASP A 420 0 SHEET 2 AB 6 SER A 423 LEU A 426 -1 O SER A 423 N LEU A 419 SHEET 3 AB 6 ILE A 457 GLU A 465 -1 O LEU A 458 N LEU A 426 SHEET 4 AB 6 ARG A 521 MET A 526 -1 O MET A 526 N ASP A 464 SHEET 5 AB 6 THR A 513 THR A 518 -1 O PHE A 514 N LEU A 525 SHEET 6 AB 6 ARG A 505 ALA A 508 -1 O ARG A 505 N HIS A 517 CISPEP 1 GLY A 481 PRO A 482 0 -4.30 SITE 1 AC1 4 SER A 431 GLU A 432 ASP A 433 ARG A 521 SITE 1 AC2 3 LYS A 467 ARG A 472 ARG A 474 CRYST1 34.009 67.057 67.802 90.00 90.00 90.00 P 21 21 21 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 0.029404 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014749 0.00000