HEADER TRANSFERASE 06-OCT-14 4V26 TITLE VER-246608, A NOVEL PAN-ISOFORM ATP COMPETITIVE INHIBITOR OF PYRUVATE TITLE 2 DEHYDROGENASE KINASE, DISRUPTS WARBURG METABOLISM AND INDUCES TITLE 3 CONTEXT- DEPENDENT CYTOSTASIS IN CANCER CELLS COMPND MOL_ID: 1; COMPND 2 MOLECULE: [PYRUVATE DEHYDROGENASE (ACETYL-TRANSFERRING)] KINASE COMPND 3 ISOZYME 2, MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: KINASE DOMAIN; COMPND 6 SYNONYM: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2, PDH KINASE 2, PDKI COMPND 7 I; COMPND 8 EC: 2.7.11.2; COMPND 9 ENGINEERED: 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) KEYWDS TRANSFERASE, GLYCOLYSIS, WARBURG METABOLISM, NOV3R EXPDTA X-RAY DIFFRACTION AUTHOR J.D.MOORE,A.STANISZEWSKA,T.SHAW,J.D'ALESSANDRO,B.DAVIS,A.SURGENOR, AUTHOR 2 L.BAKER,N.MATASSOVA,J.MURRAY,A.MACIAS,P.BROUGH,M.WOOD,P.C.MAHON REVDAT 4 09-OCT-19 4V26 1 JRNL REVDAT 3 05-JUL-17 4V26 1 REMARK REVDAT 2 28-JAN-15 4V26 1 JRNL REVDAT 1 03-DEC-14 4V26 0 JRNL AUTH J.D.MOORE,A.STANISZEWSKA,T.SHAW,J.D'ALESSANDRO,B.DAVIS, JRNL AUTH 2 A.SURGENOR,L.BAKER,N.MATASSOVA,J.MURRAY,A.MACIAS,P.BROUGH, JRNL AUTH 3 M.WOOD,P.C.MAHON JRNL TITL VER-246608, A NOVEL PAN-ISOFORM ATP COMPETITIVE INHIBITOR OF JRNL TITL 2 PYRUVATE DEHYDROGENASE KINASE, DISRUPTS WARBURG METABOLISM JRNL TITL 3 AND INDUCES CONTEXT-DEPENDENT CYTOSTASIS IN CANCER CELLS. JRNL REF ONCOTARGET V. 5 12862 2014 JRNL REFN ESSN 1949-2553 JRNL PMID 25404640 JRNL DOI 10.18632/ONCOTARGET.2656 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 18674 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1002 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) : 2.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1335 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2753 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 67 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -1.15000 REMARK 3 B12 (A**2) : 0.35000 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): 0.298 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.682 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2886 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3907 ; 2.073 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 6.950 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;34.321 ;24.016 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 492 ;18.686 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.239 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 425 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2176 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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. REMARK 4 REMARK 4 4V26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-14. REMARK 100 THE DEPOSITION ID IS D_1290061925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CU FILTER REMARK 200 OPTICS : OSMIC BLUE REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.50 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.550 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: APO PDK2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 28.13367 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 56.26733 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 0.00000 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 28.13367 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 56.26733 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.1 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 -1.000000 0.000000 0.000000 54.41900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -94.25647 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 MET A -7 REMARK 465 ARG A -6 REMARK 465 TRP A -5 REMARK 465 VAL A -4 REMARK 465 TRP A -3 REMARK 465 ALA A -2 REMARK 465 LEU A -1 REMARK 465 LEU A 0 REMARK 465 LYS A 1 REMARK 465 ASN A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 SER A 34 REMARK 465 GLY A 170 REMARK 465 SER A 171 REMARK 465 THR A 172 REMARK 465 ASN A 173 REMARK 465 PRO A 174 REMARK 465 ALA A 175 REMARK 465 HIS A 176 REMARK 465 THR A 305 REMARK 465 PRO A 306 REMARK 465 GLN A 307 REMARK 465 PRO A 308 REMARK 465 GLY A 309 REMARK 465 THR A 310 REMARK 465 GLY A 311 REMARK 465 GLY A 312 REMARK 465 THR A 313 REMARK 465 ASN A 367 REMARK 465 LYS A 368 REMARK 465 SER A 369 REMARK 465 ALA A 370 REMARK 465 TRP A 371 REMARK 465 ARG A 372 REMARK 465 HIS A 373 REMARK 465 TYR A 374 REMARK 465 GLN A 375 REMARK 465 THR A 376 REMARK 465 ILE A 377 REMARK 465 GLN A 378 REMARK 465 GLU A 379 REMARK 465 ALA A 380 REMARK 465 GLY A 381 REMARK 465 ASP A 382 REMARK 465 TRP A 383 REMARK 465 CYS A 384 REMARK 465 VAL A 385 REMARK 465 PRO A 386 REMARK 465 SER A 387 REMARK 465 THR A 388 REMARK 465 GLU A 389 REMARK 465 PRO A 390 REMARK 465 LYS A 391 REMARK 465 ASN A 392 REMARK 465 THR A 393 REMARK 465 SER A 394 REMARK 465 THR A 395 REMARK 465 TYR A 396 REMARK 465 ARG A 397 REMARK 465 VAL A 398 REMARK 465 SER A 399 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 ALA A 6 CB REMARK 470 ASN A 35 CG OD1 ND2 REMARK 470 GLN A 77 CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE2 PHE A 339 CE2 PHE A 339 4545 1.86 REMARK 500 OD2 ASP A 131 OD2 ASP A 195 2545 2.18 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 CYS A 37 CA - CB - SG ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 335 CB - CG - OD1 ANGL. DEV. = 5.6 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 ALA A 36 77.92 -44.84 REMARK 500 CYS A 37 33.41 -71.50 REMARK 500 PHE A 168 50.71 -100.41 REMARK 500 LYS A 178 -99.35 28.94 REMARK 500 SER A 224 -45.29 -29.02 REMARK 500 LEU A 260 -62.60 -95.24 REMARK 500 GLU A 274 -37.61 -133.24 REMARK 500 PHE A 344 -73.44 -135.42 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 MET A 209 ALA A 210 143.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TF3 A 1367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1368 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1369 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7TJ A 1370 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V25 RELATED DB: PDB REMARK 900 VER-246608, A NOVEL PAN-ISOFORM ATP COMPETITIVE INHIBITOR OF REMARK 900 PYRUVATE DEHYDROGENASE KINASE, DISRUPTS WARBURG METABOLISM AND REMARK 900 INDUCES CONTEXT-DEPENDENT CYTOSTASIS IN CANCER CELLS DBREF 4V26 A -7 399 UNP Q15119 PDK2_HUMAN 1 407 SEQADV 4V26 SER A 7 UNP Q15119 GLY 15 CONFLICT SEQRES 1 A 407 MET ARG TRP VAL TRP ALA LEU LEU LYS ASN ALA SER LEU SEQRES 2 A 407 ALA SER ALA PRO LYS TYR ILE GLU HIS PHE SER LYS PHE SEQRES 3 A 407 SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP PHE SEQRES 4 A 407 GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR PHE SEQRES 5 A 407 LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE MET SEQRES 6 A 407 LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER THR SEQRES 7 A 407 PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SER SEQRES 8 A 407 LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO GLU SEQRES 9 A 407 ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU VAL SEQRES 10 A 407 THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR MET SEQRES 11 A 407 ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY ASP SEQRES 12 A 407 ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU ASP SEQRES 13 A 407 ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU ILE SEQRES 14 A 407 ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN PRO SEQRES 15 A 407 ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN CYS SEQRES 16 A 407 ASN VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET ALA SEQRES 17 A 407 LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO ASP SEQRES 18 A 407 LEU GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS GLN SEQRES 19 A 407 PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR HIS SEQRES 20 A 407 MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA THR SEQRES 21 A 407 VAL GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO ILE SEQRES 22 A 407 LYS VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER ILE SEQRES 23 A 407 LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG LYS SEQRES 24 A 407 ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA PRO SEQRES 25 A 407 THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA GLY SEQRES 26 A 407 PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA LYS SEQRES 27 A 407 TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU GLY SEQRES 28 A 407 PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SER SEQRES 29 A 407 THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SER SEQRES 30 A 407 ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY ASP SEQRES 31 A 407 TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER THR SEQRES 32 A 407 TYR ARG VAL SER HET TF3 A1367 25 HET MG A1368 1 HET MG A1369 1 HET 7TJ A1370 40 HETNAM TF3 N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL) HETNAM 2 TF3 OXY]PHENYL} ACETAMIDE HETNAM MG MAGNESIUM ION HETNAM 7TJ N-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-2,4- HETNAM 2 7TJ DIHYDROXY-N-(4-{[(TRIFLUOROACETYL) HETNAM 3 7TJ AMINO]METHYL}BENZYL)BENZAMIDE FORMUL 2 TF3 C20 H25 CL N2 O2 FORMUL 3 MG 2(MG 2+) FORMUL 5 7TJ C28 H22 CL F3 N4 O4 FORMUL 6 HOH *115(H2 O) HELIX 1 1 SER A 7 SER A 16 1 10 HELIX 2 2 SER A 24 GLY A 32 1 9 HELIX 3 3 CYS A 37 LEU A 62 1 26 HELIX 4 4 PRO A 64 SER A 69 1 6 HELIX 5 5 THR A 70 GLU A 89 1 20 HELIX 6 6 ASP A 97 HIS A 115 1 19 HELIX 7 7 ASP A 117 TYR A 133 1 17 HELIX 8 8 ASP A 136 PHE A 168 1 33 HELIX 9 9 VAL A 189 TYR A 208 1 20 HELIX 10 10 VAL A 233 SER A 255 1 23 HELIX 11 11 PRO A 288 ILE A 292 5 5 HELIX 12 12 ILE A 292 SER A 297 5 6 HELIX 13 13 PRO A 314 PHE A 318 5 5 HELIX 14 14 GLY A 321 TYR A 331 1 11 HELIX 15 15 LEU A 355 SER A 359 5 5 SHEET 1 AA 2 ASP A 184 ASN A 188 0 SHEET 2 AA 2 HIS A 229 TYR A 232 -1 O MET A 230 N CYS A 187 SHEET 1 AB 5 LEU A 214 ASN A 220 0 SHEET 2 AB 5 ILE A 265 LEU A 271 1 O ILE A 265 N GLU A 215 SHEET 3 AB 5 ASP A 275 SER A 281 -1 O SER A 277 N ALA A 270 SHEET 4 AB 5 GLY A 345 LYS A 353 -1 O ALA A 348 N MET A 280 SHEET 5 AB 5 ASP A 335 MET A 341 -1 O ASP A 335 N TYR A 351 SITE 1 AC1 7 PRO A 64 ARG A 66 VAL A 67 VAL A 126 SITE 2 AC1 7 TYR A 129 ASN A 142 ILE A 143 SITE 1 AC2 1 LEU A 338 SITE 1 AC3 1 SER A 41 SITE 1 AC4 12 LYS A 246 ASN A 247 ARG A 250 ALA A 251 SITE 2 AC4 12 GLU A 254 ASP A 282 GLY A 284 GLY A 286 SITE 3 AC4 12 VAL A 287 THR A 346 HOH A2067 HOH A2084 CRYST1 108.838 108.838 84.401 90.00 90.00 120.00 P 64 6 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 0.009188 0.005305 0.000000 0.00000 SCALE2 0.000000 0.010609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011848 0.00000