HEADER TRANSFERASE 10-JUN-07 2Q8F TITLE STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 1; COMPND 5 EC: 2.7.11.2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PDK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GHKL ATPASE/KINASE FAMILY, PYRUVATE DEHYDROGENASE COMPLEX, KEYWDS 2 MITOCHONDRIAL KINASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO,J.LI,J.L.CHUANG,D.T.CHUANG REVDAT 5 30-AUG-23 2Q8F 1 REMARK LINK REVDAT 4 13-JUL-11 2Q8F 1 VERSN REVDAT 3 24-FEB-09 2Q8F 1 VERSN REVDAT 2 28-AUG-07 2Q8F 1 JRNL REVDAT 1 24-JUL-07 2Q8F 0 JRNL AUTH M.KATO,J.LI,J.L.CHUANG,D.T.CHUANG JRNL TITL DISTINCT STRUCTURAL MECHANISMS FOR INHIBITION OF PYRUVATE JRNL TITL 2 DEHYDROGENASE KINASE ISOFORMS BY AZD7545, DICHLOROACETATE, JRNL TITL 3 AND RADICICOL. JRNL REF STRUCTURE V. 15 992 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 17683942 JRNL DOI 10.1016/J.STR.2007.07.001 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 33007 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1737 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) : 2.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.02 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2954 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 212 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.17000 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): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.884 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3039 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4120 ; 1.527 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 5.980 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;33.986 ;23.557 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 513 ;14.315 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;19.802 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2333 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1351 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2064 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 192 ; 0.132 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.249 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 51 ; 0.165 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.153 ; 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): 1829 ; 0.993 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2966 ; 1.801 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1233 ; 2.687 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1154 ; 4.169 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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: NULL REMARK 4 REMARK 4 2Q8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34783 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.53600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 1Y8P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.42 M NAK TARTRATE, 0.1 M NA CITRATE, REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 55.20150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.09500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.60075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.09500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.09500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 82.80225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.09500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.09500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.60075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.09500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.09500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 82.80225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.20150 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 300 REMARK: THE SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED REMARK 300 BY THE FOLLOWING OPERATION: Y,X,-Z 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 536 LIES ON A SPECIAL POSITION. 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 SER A 30 REMARK 465 ASP A 31 REMARK 465 SER A 32 REMARK 465 GLY A 33 REMARK 465 SER A 34 REMARK 465 SER A 35 REMARK 465 PRO A 36 REMARK 465 ALA A 37 REMARK 465 SER A 38 REMARK 465 GLU A 39 REMARK 465 ARG A 40 REMARK 465 VAL A 68 REMARK 465 ASN A 69 REMARK 465 ALA A 70 REMARK 465 GLY A 168 REMARK 465 VAL A 169 REMARK 465 GLY A 204 REMARK 465 LYS A 205 REMARK 465 GLY A 206 REMARK 465 LYS A 207 REMARK 465 GLY A 208 REMARK 465 SER A 209 REMARK 465 PRO A 210 REMARK 465 SER A 211 REMARK 465 HIS A 212 REMARK 465 ARG A 213 REMARK 465 LYS A 214 REMARK 465 HIS A 415 REMARK 465 GLU A 416 REMARK 465 SER A 424 REMARK 465 ARG A 425 REMARK 465 GLU A 426 REMARK 465 PRO A 427 REMARK 465 LYS A 428 REMARK 465 ASP A 429 REMARK 465 MET A 430 REMARK 465 THR A 431 REMARK 465 THR A 432 REMARK 465 PHE A 433 REMARK 465 ARG A 434 REMARK 465 SER A 435 REMARK 465 ALA A 436 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 128 C ALA A 129 N 0.154 REMARK 500 GLU A 130 CG GLU A 130 CD 0.113 REMARK 500 GLU A 130 CD GLU A 130 OE1 0.100 REMARK 500 GLU A 130 CD GLU A 130 OE2 0.086 REMARK 500 GLU A 130 C GLU A 130 O 0.141 REMARK 500 ASP A 131 CG ASP A 131 OD1 0.404 REMARK 500 LYS A 133 CE LYS A 133 NZ 0.336 REMARK 500 LYS A 133 C LYS A 133 O -0.149 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 ARG A 319 46.33 -108.30 REMARK 500 TYR A 381 -63.42 -126.24 REMARK 500 ASN A 404 -168.91 -164.03 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 K A 437 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 50 O REMARK 620 2 ARG A 51 O 69.3 REMARK 620 3 PHE A 52 O 81.2 67.0 REMARK 620 4 ASN A 89 OD1 88.8 141.1 78.5 REMARK 620 5 TYR A 403 O 100.6 126.7 166.1 87.7 REMARK 620 6 HOH A 510 O 131.6 63.2 88.7 135.4 100.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 437 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q8G RELATED DB: PDB REMARK 900 PDK1-AZD7545 COMPLEX REMARK 900 RELATED ID: 2Q8H RELATED DB: PDB REMARK 900 PDK1-DCA COMPLEX REMARK 900 RELATED ID: 2Q8I RELATED DB: PDB REMARK 900 PDK3-RADICICOL COMPLEX DBREF 2Q8F A 30 436 UNP Q15118 PDK1_HUMAN 30 436 SEQRES 1 A 407 SER ASP SER GLY SER SER PRO ALA SER GLU ARG GLY VAL SEQRES 2 A 407 PRO GLY GLN VAL ASP PHE TYR ALA ARG PHE SER PRO SER SEQRES 3 A 407 PRO LEU SER MET LYS GLN PHE LEU ASP PHE GLY SER VAL SEQRES 4 A 407 ASN ALA CYS GLU LYS THR SER PHE MET PHE LEU ARG GLN SEQRES 5 A 407 GLU LEU PRO VAL ARG LEU ALA ASN ILE MET LYS GLU ILE SEQRES 6 A 407 SER LEU LEU PRO ASP ASN LEU LEU ARG THR PRO SER VAL SEQRES 7 A 407 GLN LEU VAL GLN SER TRP TYR ILE GLN SER LEU GLN GLU SEQRES 8 A 407 LEU LEU ASP PHE LYS ASP LYS SER ALA GLU ASP ALA LYS SEQRES 9 A 407 ALA ILE TYR ASP PHE THR ASP THR VAL ILE ARG ILE ARG SEQRES 10 A 407 ASN ARG HIS ASN ASP VAL ILE PRO THR MET ALA GLN GLY SEQRES 11 A 407 VAL ILE GLU TYR LYS GLU SER PHE GLY VAL ASP PRO VAL SEQRES 12 A 407 THR SER GLN ASN VAL GLN TYR PHE LEU ASP ARG PHE TYR SEQRES 13 A 407 MET SER ARG ILE SER ILE ARG MET LEU LEU ASN GLN HIS SEQRES 14 A 407 SER LEU LEU PHE GLY GLY LYS GLY LYS GLY SER PRO SER SEQRES 15 A 407 HIS ARG LYS HIS ILE GLY SER ILE ASN PRO ASN CYS ASN SEQRES 16 A 407 VAL LEU GLU VAL ILE LYS ASP GLY TYR GLU ASN ALA ARG SEQRES 17 A 407 ARG LEU CYS ASP LEU TYR TYR ILE ASN SER PRO GLU LEU SEQRES 18 A 407 GLU LEU GLU GLU LEU ASN ALA LYS SER PRO GLY GLN PRO SEQRES 19 A 407 ILE GLN VAL VAL TYR VAL PRO SER HIS LEU TYR HIS MET SEQRES 20 A 407 VAL PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR MET SEQRES 21 A 407 GLU HIS HIS ALA ASN ARG GLY VAL TYR PRO PRO ILE GLN SEQRES 22 A 407 VAL HIS VAL THR LEU GLY ASN GLU ASP LEU THR VAL LYS SEQRES 23 A 407 MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS ILE SEQRES 24 A 407 ASP ARG LEU PHE ASN TYR MET TYR SER THR ALA PRO ARG SEQRES 25 A 407 PRO ARG VAL GLU THR SER ARG ALA VAL PRO LEU ALA GLY SEQRES 26 A 407 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA GLN SEQRES 27 A 407 TYR PHE GLN GLY ASP LEU LYS LEU TYR SER LEU GLU GLY SEQRES 28 A 407 TYR GLY THR ASP ALA VAL ILE TYR ILE LYS ALA LEU SER SEQRES 29 A 407 THR ASP SER ILE GLU ARG LEU PRO VAL TYR ASN LYS ALA SEQRES 30 A 407 ALA TRP LYS HIS TYR ASN THR ASN HIS GLU ALA ASP ASP SEQRES 31 A 407 TRP CYS VAL PRO SER ARG GLU PRO LYS ASP MET THR THR SEQRES 32 A 407 PHE ARG SER ALA HET K A 437 1 HETNAM K POTASSIUM ION FORMUL 2 K K 1+ FORMUL 3 HOH *212(H2 O) HELIX 1 1 GLY A 41 ARG A 51 1 11 HELIX 2 2 SER A 58 SER A 67 1 10 HELIX 3 3 CYS A 71 SER A 95 1 25 HELIX 4 4 PRO A 98 ARG A 103 1 6 HELIX 5 5 THR A 104 LEU A 122 1 19 HELIX 6 6 ASP A 123 LYS A 125 5 3 HELIX 7 7 ASP A 131 HIS A 149 1 19 HELIX 8 8 ASP A 151 PHE A 167 1 17 HELIX 9 9 PRO A 171 GLY A 203 1 33 HELIX 10 10 VAL A 225 ILE A 245 1 21 HELIX 11 11 VAL A 269 HIS A 292 1 24 HELIX 12 12 PRO A 324 ASP A 329 1 6 HELIX 13 13 ARG A 330 ASN A 333 5 4 HELIX 14 14 TYR A 357 PHE A 369 1 13 HELIX 15 15 ASN A 404 ASN A 412 1 9 SHEET 1 A 2 ASN A 220 ASN A 224 0 SHEET 2 A 2 GLN A 265 TYR A 268 -1 O TYR A 268 N ASN A 220 SHEET 1 B 5 LEU A 250 ASN A 256 0 SHEET 2 B 5 ILE A 301 LEU A 307 1 O VAL A 305 N GLU A 253 SHEET 3 B 5 ASP A 311 ASP A 318 -1 O SER A 317 N GLN A 302 SHEET 4 B 5 GLY A 382 LYS A 390 -1 O ILE A 389 N LEU A 312 SHEET 5 B 5 ASP A 372 LEU A 378 -1 N LYS A 374 O VAL A 386 LINK O ALA A 50 K K A 437 1555 1555 2.34 LINK O ARG A 51 K K A 437 1555 1555 3.61 LINK O PHE A 52 K K A 437 1555 1555 2.72 LINK OD1 ASN A 89 K K A 437 1555 1555 2.65 LINK O TYR A 403 K K A 437 1555 1555 2.51 LINK K K A 437 O HOH A 510 1555 1555 2.73 SITE 1 AC1 7 ALA A 50 ARG A 51 PHE A 52 ASN A 89 SITE 2 AC1 7 VAL A 402 TYR A 403 HOH A 510 CRYST1 98.190 98.190 110.403 90.00 90.00 90.00 P 41 21 2 8 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 0.010184 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010184 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009058 0.00000