HEADER TRANSFERASE 10-JUN-07 2Q8I TITLE PYRUVATE DEHYDROGENASE KINASE ISOFORM 3 IN COMPLEX WITH ANTITUMOR DRUG TITLE 2 RADICICOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 3; COMPND 5 EC: 2.7.11.2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DIHYDROLIPOYLLYSINE-RESIDUE ACETYLTRANSFERASE COMPONENT OF COMPND 9 PYRUVATE DEHYDROGENASE COMPLEX; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: LIPOYL-BEARING DOMAIN; COMPND 12 SYNONYM: PYRUVATE DEHYDROGENASE COMPLEX E2 SUBUNIT, PDCE2, E2, COMPND 13 DIHYDROLIPOAMIDE S-ACETYLTRANSFERASE COMPONENT OF PYRUVATE COMPND 14 DEHYDROGENASE COMPLEX, PDC-E2, 70 KDA MITOCHONDRIAL AUTOANTIGEN OF COMPND 15 PRIMARY BILIARY CIRRHOSIS, PBC, M2 ANTIGEN COMPLEX 70 KDA SUBUNIT; COMPND 16 EC: 2.3.1.12; COMPND 17 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: PDK3; 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; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: DLAT, DLTA; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GHKL ATPASE/KINASE FAMILY, PYRUVATE DEHYDROGENASE COMPLEX, KEYWDS 2 MITOCHONDRIAL KINASE, RADICICOL, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KATO,J.LI,J.L.CHUANG,D.T.CHUANG REVDAT 7 16-OCT-24 2Q8I 1 REMARK REVDAT 6 30-AUG-23 2Q8I 1 REMARK SEQADV LINK REVDAT 5 18-OCT-17 2Q8I 1 REMARK REVDAT 4 13-JUL-11 2Q8I 1 VERSN REVDAT 3 24-FEB-09 2Q8I 1 VERSN REVDAT 2 28-AUG-07 2Q8I 1 JRNL REVDAT 1 24-JUL-07 2Q8I 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. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 32534 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2227 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3330 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3727 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.03000 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): 0.271 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.157 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.535 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3875 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5250 ; 1.820 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 460 ; 6.671 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;35.817 ;24.078 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 665 ;19.589 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.913 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 570 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2944 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1598 ; 0.234 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2611 ; 0.323 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 149 ; 0.116 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.193 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 58 ; 0.192 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 22 ; 0.172 ; 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): 2321 ; 0.897 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3770 ; 1.693 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1581 ; 2.696 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1477 ; 4.193 ; 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 2Q8I 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_1000043282. 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 : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-3 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32612 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.69400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2Q8F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SOUDIUM CITRATE, SODIUM POTASSIUM REMARK 280 PHOSPHATE, SODIUM CHROLIDE, PH 5.6, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 159.75800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.87900 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 119.81850 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.93950 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 199.69750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 159.75800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 79.87900 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 39.93950 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 119.81850 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 199.69750 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,Y,1/2-Z, OF BOTH THE CHAIN A AND B. 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 -1.000000 0.000000 0.000000 -120.87200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 119.81850 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 -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 GLY A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 ARG A 0 REMARK 465 LEU A 1 REMARK 465 GLU A 2 REMARK 465 ASN A 3 REMARK 465 LEU A 4 REMARK 465 TYR A 5 REMARK 465 PHE A 6 REMARK 465 GLN A 7 REMARK 465 GLY A 8 REMARK 465 LYS A 9 REMARK 465 GLN A 10 REMARK 465 PRO A 11 REMARK 465 VAL A 12 REMARK 465 GLY A 174 REMARK 465 ASP A 175 REMARK 465 THR A 307 REMARK 465 ALA A 308 REMARK 465 PRO A 309 REMARK 465 ARG A 310 REMARK 465 PRO A 311 REMARK 465 SER A 312 REMARK 465 LEU A 313 REMARK 465 GLU A 314 REMARK 465 PRO A 315 REMARK 465 THR A 316 REMARK 465 ARG A 317 REMARK 465 ALA A 318 REMARK 465 ALA A 319 REMARK 465 PRO A 320 REMARK 465 LEU A 321 REMARK 465 ALA A 322 REMARK 465 GLY A 323 REMARK 465 PHE A 324 REMARK 465 TYR A 402 REMARK 465 LYS A 403 REMARK 465 ALA A 404 REMARK 465 LYS A 405 REMARK 465 GLN A 406 REMARK 465 GLY B 106 REMARK 465 GLY B 107 REMARK 465 SER B 108 REMARK 465 HIS B 109 REMARK 465 HIS B 110 REMARK 465 HIS B 111 REMARK 465 HIS B 112 REMARK 465 HIS B 113 REMARK 465 HIS B 114 REMARK 465 GLY B 115 REMARK 465 MET B 116 REMARK 465 ALA B 117 REMARK 465 ARG B 118 REMARK 465 LEU B 119 REMARK 465 GLU B 120 REMARK 465 ASN B 121 REMARK 465 LEU B 122 REMARK 465 TYR B 123 REMARK 465 PHE B 124 REMARK 465 GLN B 125 REMARK 465 GLY B 126 REMARK 465 SER B 127 REMARK 465 ARG B 221 REMARK 465 PRO B 222 REMARK 465 THR B 223 REMARK 465 GLU B 224 REMARK 465 VAL B 225 REMARK 465 THR B 226 REMARK 465 ASP B 227 REMARK 465 LEU B 228 REMARK 465 LYS B 229 REMARK 465 PRO B 230 REMARK 465 GLN B 231 REMARK 465 VAL B 232 REMARK 465 PRO B 233 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 THR A 176 OG1 CG2 REMARK 470 ASN A 177 CG OD1 ND2 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 TYR A 267 CE1 TYR A 267 CZ -0.081 REMARK 500 SER B 128 CB SER B 128 OG 0.101 REMARK 500 PRO B 130 CD PRO B 130 N 0.173 REMARK 500 LYS B 210 CE LYS B 210 NZ 0.242 REMARK 500 ASP B 213 C ASP B 213 O 0.129 REMARK 500 ALA B 216 C PHE B 217 N 0.171 REMARK 500 PHE B 217 CZ PHE B 217 CE2 0.194 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 332 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 336 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LEU A 344 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 ASP B 172 N - CA - CB ANGL. DEV. = -11.2 DEGREES REMARK 500 LYS B 210 CD - CE - NZ ANGL. DEV. = -14.6 DEGREES REMARK 500 PHE B 217 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 PHE B 217 CD1 - CG - CD2 ANGL. DEV. = 8.9 DEGREES REMARK 500 PHE B 217 CB - CG - CD1 ANGL. DEV. = -4.8 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 ASN A 39 -85.11 -84.83 REMARK 500 GLU A 100 22.83 -73.41 REMARK 500 VAL A 179 -88.53 -54.47 REMARK 500 PHE A 338 42.34 -108.18 REMARK 500 VAL A 350 -59.44 -128.40 REMARK 500 ASN A 373 -172.63 -171.17 REMARK 500 ASP A 388 -38.68 -18.97 REMARK 500 GLU B 193 130.34 -37.43 REMARK 500 ALA B 216 2.13 -52.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP A 387 ASP A 388 143.98 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 407 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 20 O REMARK 620 2 PHE A 22 O 92.6 REMARK 620 3 ASN A 59 OD1 80.4 90.0 REMARK 620 4 PHE A 372 O 89.7 174.7 85.6 REMARK 620 N 1 2 3 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 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RED B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RDC A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q8F RELATED DB: PDB REMARK 900 RELATED ID: 2Q8G RELATED DB: PDB REMARK 900 RELATED ID: 2Q8H RELATED DB: PDB DBREF 2Q8I A 9 406 UNP Q15120 PDK3_HUMAN 9 406 DBREF 2Q8I B 126 233 UNP P10515 ODP2_HUMAN 179 286 SEQADV 2Q8I GLY A -12 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I GLY A -11 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I SER A -10 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I HIS A -9 UNP Q15120 EXPRESSION TAG SEQADV 2Q8I HIS A -8 UNP Q15120 EXPRESSION TAG SEQADV 2Q8I HIS A -7 UNP Q15120 EXPRESSION TAG SEQADV 2Q8I HIS A -6 UNP Q15120 EXPRESSION TAG SEQADV 2Q8I HIS A -5 UNP Q15120 EXPRESSION TAG SEQADV 2Q8I HIS A -4 UNP Q15120 EXPRESSION TAG SEQADV 2Q8I GLY A -3 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I MET A -2 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I ALA A -1 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I ARG A 0 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I LEU A 1 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I GLU A 2 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I ASN A 3 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I LEU A 4 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I TYR A 5 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I PHE A 6 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I GLN A 7 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I GLY A 8 UNP Q15120 CLONING ARTIFACT SEQADV 2Q8I GLY B 106 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I GLY B 107 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I SER B 108 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I HIS B 109 UNP P10515 EXPRESSION TAG SEQADV 2Q8I HIS B 110 UNP P10515 EXPRESSION TAG SEQADV 2Q8I HIS B 111 UNP P10515 EXPRESSION TAG SEQADV 2Q8I HIS B 112 UNP P10515 EXPRESSION TAG SEQADV 2Q8I HIS B 113 UNP P10515 EXPRESSION TAG SEQADV 2Q8I HIS B 114 UNP P10515 EXPRESSION TAG SEQADV 2Q8I GLY B 115 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I MET B 116 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I ALA B 117 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I ARG B 118 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I LEU B 119 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I GLU B 120 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I ASN B 121 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I LEU B 122 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I TYR B 123 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I PHE B 124 UNP P10515 CLONING ARTIFACT SEQADV 2Q8I GLN B 125 UNP P10515 CLONING ARTIFACT SEQRES 1 A 419 GLY GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA ARG SEQRES 2 A 419 LEU GLU ASN LEU TYR PHE GLN GLY LYS GLN PRO VAL PRO SEQRES 3 A 419 LYS GLN ILE GLU ARG TYR SER ARG PHE SER PRO SER PRO SEQRES 4 A 419 LEU SER ILE LYS GLN PHE LEU ASP PHE GLY ARG ASP ASN SEQRES 5 A 419 ALA CYS GLU LYS THR SER TYR MET PHE LEU ARG LYS GLU SEQRES 6 A 419 LEU PRO VAL ARG LEU ALA ASN THR MET ARG GLU VAL ASN SEQRES 7 A 419 LEU LEU PRO ASP ASN LEU LEU ASN ARG PRO SER VAL GLY SEQRES 8 A 419 LEU VAL GLN SER TRP TYR MET GLN SER PHE LEU GLU LEU SEQRES 9 A 419 LEU GLU TYR GLU ASN LYS SER PRO GLU ASP PRO GLN VAL SEQRES 10 A 419 LEU ASP ASN PHE LEU GLN VAL LEU ILE LYS VAL ARG ASN SEQRES 11 A 419 ARG HIS ASN ASP VAL VAL PRO THR MET ALA GLN GLY VAL SEQRES 12 A 419 ILE GLU TYR LYS GLU LYS PHE GLY PHE ASP PRO PHE ILE SEQRES 13 A 419 SER THR ASN ILE GLN TYR PHE LEU ASP ARG PHE TYR THR SEQRES 14 A 419 ASN ARG ILE SER PHE ARG MET LEU ILE ASN GLN HIS THR SEQRES 15 A 419 LEU LEU PHE GLY GLY ASP THR ASN PRO VAL HIS PRO LYS SEQRES 16 A 419 HIS ILE GLY SER ILE ASP PRO THR CYS ASN VAL ALA ASP SEQRES 17 A 419 VAL VAL LYS ASP ALA TYR GLU THR ALA LYS MET LEU CYS SEQRES 18 A 419 GLU GLN TYR TYR LEU VAL ALA PRO GLU LEU GLU VAL GLU SEQRES 19 A 419 GLU PHE ASN ALA LYS ALA PRO ASP LYS PRO ILE GLN VAL SEQRES 20 A 419 VAL TYR VAL PRO SER HIS LEU PHE HIS MET LEU PHE GLU SEQRES 21 A 419 LEU PHE LYS ASN SER MET ARG ALA THR VAL GLU LEU TYR SEQRES 22 A 419 GLU ASP ARG LYS GLU GLY TYR PRO ALA VAL LYS THR LEU SEQRES 23 A 419 VAL THR LEU GLY LYS GLU ASP LEU SER ILE LYS ILE SER SEQRES 24 A 419 ASP LEU GLY GLY GLY VAL PRO LEU ARG LYS ILE ASP ARG SEQRES 25 A 419 LEU PHE ASN TYR MET TYR SER THR ALA PRO ARG PRO SER SEQRES 26 A 419 LEU GLU PRO THR ARG ALA ALA PRO LEU ALA GLY PHE GLY SEQRES 27 A 419 TYR GLY LEU PRO ILE SER ARG LEU TYR ALA ARG TYR PHE SEQRES 28 A 419 GLN GLY ASP LEU LYS LEU TYR SER MET GLU GLY VAL GLY SEQRES 29 A 419 THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER SER GLU SEQRES 30 A 419 SER PHE GLU ARG LEU PRO VAL PHE ASN LYS SER ALA TRP SEQRES 31 A 419 ARG HIS TYR LYS THR THR PRO GLU ALA ASP ASP TRP SER SEQRES 32 A 419 ASN PRO SER SER GLU PRO ARG ASP ALA SER LYS TYR LYS SEQRES 33 A 419 ALA LYS GLN SEQRES 1 B 128 GLY GLY SER HIS HIS HIS HIS HIS HIS GLY MET ALA ARG SEQRES 2 B 128 LEU GLU ASN LEU TYR PHE GLN GLY SER SER TYR PRO PRO SEQRES 3 B 128 HIS MET GLN VAL LEU LEU PRO ALA LEU SER PRO THR MET SEQRES 4 B 128 THR MET GLY THR VAL GLN ARG TRP GLU LYS LYS VAL GLY SEQRES 5 B 128 GLU LYS LEU SER GLU GLY ASP LEU LEU ALA GLU ILE GLU SEQRES 6 B 128 THR ASP LYS ALA THR ILE GLY PHE GLU VAL GLN GLU GLU SEQRES 7 B 128 GLY TYR LEU ALA LYS ILE LEU VAL PRO GLU GLY THR ARG SEQRES 8 B 128 ASP VAL PRO LEU GLY THR PRO LEU CYS ILE ILE VAL GLU SEQRES 9 B 128 LYS GLU ALA ASP ILE SER ALA PHE ALA ASP TYR ARG PRO SEQRES 10 B 128 THR GLU VAL THR ASP LEU LYS PRO GLN VAL PRO HET K A 407 1 HET RDC A 408 25 HET GOL A 409 6 HET RED B 300 11 HETNAM K POTASSIUM ION HETNAM RDC RADICICOL HETNAM GOL GLYCEROL HETNAM RED DIHYDROLIPOIC ACID HETSYN RDC MONORDEN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 K K 1+ FORMUL 4 RDC C18 H17 CL O6 FORMUL 5 GOL C3 H8 O3 FORMUL 6 RED C8 H16 O2 S2 FORMUL 7 HOH *81(H2 O) HELIX 1 1 PRO A 13 PHE A 22 1 10 HELIX 2 2 SER A 28 ASN A 39 1 12 HELIX 3 3 CYS A 41 ASN A 65 1 25 HELIX 4 4 PRO A 68 ASN A 73 1 6 HELIX 5 5 ARG A 74 GLU A 93 1 20 HELIX 6 6 ASP A 101 HIS A 119 1 19 HELIX 7 7 ASP A 121 GLY A 138 1 18 HELIX 8 8 ASP A 140 GLY A 173 1 34 HELIX 9 9 VAL A 193 LEU A 213 1 21 HELIX 10 10 VAL A 237 GLU A 261 1 25 HELIX 11 11 PRO A 293 ASN A 302 5 10 HELIX 12 12 TYR A 326 PHE A 338 1 13 HELIX 13 13 LEU A 361 SER A 365 5 5 HELIX 14 14 ASN A 373 THR A 382 1 10 HELIX 15 15 LYS B 210 ALA B 218 5 9 SHEET 1 A 2 ASP A 188 ASN A 192 0 SHEET 2 A 2 GLN A 233 TYR A 236 -1 O TYR A 236 N ASP A 188 SHEET 1 B 5 LEU A 218 ASN A 224 0 SHEET 2 B 5 VAL A 270 LEU A 276 1 O THR A 272 N GLU A 221 SHEET 3 B 5 ASP A 280 ASP A 287 -1 O SER A 286 N LYS A 271 SHEET 4 B 5 GLY A 351 LYS A 359 -1 O ALA A 354 N ILE A 285 SHEET 5 B 5 ASP A 341 MET A 347 -1 N LYS A 343 O VAL A 355 SHEET 1 C 4 HIS B 132 LEU B 136 0 SHEET 2 C 4 PRO B 203 VAL B 208 -1 O LEU B 204 N VAL B 135 SHEET 3 C 4 GLY B 184 ILE B 189 -1 N ALA B 187 O ILE B 206 SHEET 4 C 4 LYS B 159 LEU B 160 -1 N LEU B 160 O GLY B 184 SHEET 1 D 4 THR B 175 GLU B 179 0 SHEET 2 D 4 LEU B 165 GLU B 170 -1 N ALA B 167 O PHE B 178 SHEET 3 D 4 MET B 146 TRP B 152 -1 N THR B 148 O GLU B 170 SHEET 4 D 4 VAL B 198 PRO B 199 -1 O VAL B 198 N GLY B 147 LINK NZ LYS B 173 C1 RED B 300 1555 1555 1.32 LINK O SER A 20 K K A 407 1555 1555 2.70 LINK O PHE A 22 K K A 407 1555 1555 2.56 LINK OD1 ASN A 59 K K A 407 1555 1555 2.87 LINK O PHE A 372 K K A 407 1555 1555 2.56 SITE 1 AC1 5 SER A 20 ARG A 21 PHE A 22 ASN A 59 SITE 2 AC1 5 PHE A 372 SITE 1 AC2 3 PHE A 48 ARG A 397 LYS B 173 SITE 1 AC3 12 LEU A 248 ASN A 251 SER A 252 ALA A 255 SITE 2 AC3 12 ASP A 287 VAL A 292 LEU A 300 LEU A 328 SITE 3 AC3 12 THR A 352 HOH A 431 HOH A 453 HOH A 475 SITE 1 AC4 5 PHE A 301 LYS A 343 LEU A 344 TYR A 345 SITE 2 AC4 5 HOH A 419 CRYST1 120.872 120.872 239.637 90.00 90.00 120.00 P 65 2 2 12 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 0.008273 0.004777 0.000000 0.00000 SCALE2 0.000000 0.009553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004173 0.00000