HEADER TRANSFERASE 06-OCT-14 4V25 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 5 01-MAY-24 4V25 1 REMARK REVDAT 4 09-OCT-19 4V25 1 JRNL REVDAT 3 05-JUL-17 4V25 1 REMARK REVDAT 2 28-JAN-15 4V25 1 JRNL REVDAT 1 03-DEC-14 4V25 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. 2.60 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 16403 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 872 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) : 1194 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.94000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : -3.04000 REMARK 3 B12 (A**2) : 0.94000 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): 0.405 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.286 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.241 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.022 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2880 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2727 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3897 ; 1.738 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6239 ; 0.885 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 7.308 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 127 ;35.902 ;24.016 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 492 ;18.998 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;15.227 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 424 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3182 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 636 ; 0.001 ; 0.020 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 4V25 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_1290061923. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-12 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 : 17281 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.310 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 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) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.19 REMARK 200 R MERGE FOR SHELL (I) : 0.53000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: APO PDK2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE PH 5.8, 0.125 M REMARK 280 MAGNESIUM CHLORIDE AND 6% ISOPROPANOL, 4OC 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 28.12667 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 56.25333 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 28.12667 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 56.25333 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: 2650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.9 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 54.47200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -94.34827 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 -8 REMARK 465 ARG A -7 REMARK 465 TRP A -6 REMARK 465 VAL A -5 REMARK 465 TRP A -4 REMARK 465 ALA A -3 REMARK 465 LEU A -2 REMARK 465 LEU A -1 REMARK 465 LYS A 0 REMARK 465 ASN A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 SER A 34 REMARK 465 ASN A 35 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 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 OD2 ASP A 131 OD2 ASP A 195 2545 2.16 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 ASP A 335 CB - CG - OD1 ANGL. DEV. = 5.5 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 HIS A 98 6.82 -49.33 REMARK 500 PHE A 168 67.26 -104.50 REMARK 500 LYS A 178 -113.56 28.22 REMARK 500 ASN A 223 75.95 -107.43 REMARK 500 SER A 224 -59.06 28.83 REMARK 500 LYS A 225 3.57 -150.49 REMARK 500 LEU A 260 -75.37 -95.63 REMARK 500 ILE A 261 129.56 -38.49 REMARK 500 GLU A 274 -28.25 -140.59 REMARK 500 ARG A 283 59.40 -106.17 REMARK 500 LEU A 315 37.67 -91.28 REMARK 500 PHE A 332 54.53 -118.36 REMARK 500 PHE A 344 -61.99 -140.56 REMARK 500 VAL A 365 -109.76 -89.99 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 210 147.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2063 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A2064 DISTANCE = 6.94 ANGSTROMS 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 SZ6 A 1369 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4V26 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 4V25 A -8 399 UNP Q15119 PDK2_HUMAN 1 407 SEQADV 4V25 SER A 7 UNP P10725 INSERTION SEQRES 1 A 408 MET ARG TRP VAL TRP ALA LEU LEU LYS ASN ALA SER LEU SEQRES 2 A 408 ALA GLY SER ALA PRO LYS TYR ILE GLU HIS PHE SER LYS SEQRES 3 A 408 PHE SER PRO SER PRO LEU SER MET LYS GLN PHE LEU ASP SEQRES 4 A 408 PHE GLY SER SER ASN ALA CYS GLU LYS THR SER PHE THR SEQRES 5 A 408 PHE LEU ARG GLN GLU LEU PRO VAL ARG LEU ALA ASN ILE SEQRES 6 A 408 MET LYS GLU ILE ASN LEU LEU PRO ASP ARG VAL LEU SER SEQRES 7 A 408 THR PRO SER VAL GLN LEU VAL GLN SER TRP TYR VAL GLN SEQRES 8 A 408 SER LEU LEU ASP ILE MET GLU PHE LEU ASP LYS ASP PRO SEQRES 9 A 408 GLU ASP HIS ARG THR LEU SER GLN PHE THR ASP ALA LEU SEQRES 10 A 408 VAL THR ILE ARG ASN ARG HIS ASN ASP VAL VAL PRO THR SEQRES 11 A 408 MET ALA GLN GLY VAL LEU GLU TYR LYS ASP THR TYR GLY SEQRES 12 A 408 ASP ASP PRO VAL SER ASN GLN ASN ILE GLN TYR PHE LEU SEQRES 13 A 408 ASP ARG PHE TYR LEU SER ARG ILE SER ILE ARG MET LEU SEQRES 14 A 408 ILE ASN GLN HIS THR LEU ILE PHE ASP GLY SER THR ASN SEQRES 15 A 408 PRO ALA HIS PRO LYS HIS ILE GLY SER ILE ASP PRO ASN SEQRES 16 A 408 CYS ASN VAL SER GLU VAL VAL LYS ASP ALA TYR ASP MET SEQRES 17 A 408 ALA LYS LEU LEU CYS ASP LYS TYR TYR MET ALA SER PRO SEQRES 18 A 408 ASP LEU GLU ILE GLN GLU ILE ASN ALA ALA ASN SER LYS SEQRES 19 A 408 GLN PRO ILE HIS MET VAL TYR VAL PRO SER HIS LEU TYR SEQRES 20 A 408 HIS MET LEU PHE GLU LEU PHE LYS ASN ALA MET ARG ALA SEQRES 21 A 408 THR VAL GLU SER HIS GLU SER SER LEU ILE LEU PRO PRO SEQRES 22 A 408 ILE LYS VAL MET VAL ALA LEU GLY GLU GLU ASP LEU SER SEQRES 23 A 408 ILE LYS MET SER ASP ARG GLY GLY GLY VAL PRO LEU ARG SEQRES 24 A 408 LYS ILE GLU ARG LEU PHE SER TYR MET TYR SER THR ALA SEQRES 25 A 408 PRO THR PRO GLN PRO GLY THR GLY GLY THR PRO LEU ALA SEQRES 26 A 408 GLY PHE GLY TYR GLY LEU PRO ILE SER ARG LEU TYR ALA SEQRES 27 A 408 LYS TYR PHE GLN GLY ASP LEU GLN LEU PHE SER MET GLU SEQRES 28 A 408 GLY PHE GLY THR ASP ALA VAL ILE TYR LEU LYS ALA LEU SEQRES 29 A 408 SER THR ASP SER VAL GLU ARG LEU PRO VAL TYR ASN LYS SEQRES 30 A 408 SER ALA TRP ARG HIS TYR GLN THR ILE GLN GLU ALA GLY SEQRES 31 A 408 ASP TRP CYS VAL PRO SER THR GLU PRO LYS ASN THR SER SEQRES 32 A 408 THR TYR ARG VAL SER HET TF3 A1367 25 HET MG A1368 1 HET SZ6 A1369 39 HETNAM TF3 N-(2-AMINOETHYL)-2-{3-CHLORO-4-[(4-ISOPROPYLBENZYL) HETNAM 2 TF3 OXY]PHENYL} ACETAMIDE HETNAM MG MAGNESIUM ION HETNAM SZ6 N-[4-(2-CHLORO-5-METHYLPYRIMIDIN-4-YL)PHENYL]-N-(4- HETNAM 2 SZ6 {[(DIFLUOROACETYL)AMINO]METHYL}BENZYL)-2,4- HETNAM 3 SZ6 DIHYDROXYBENZAMIDE FORMUL 2 TF3 C20 H25 CL N2 O2 FORMUL 3 MG MG 2+ FORMUL 4 SZ6 C28 H23 CL F2 N4 O4 FORMUL 5 HOH *64(H2 O) HELIX 1 1 SER A 7 SER A 16 1 10 HELIX 2 2 SER A 24 PHE A 31 1 8 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 ARG A 99 HIS A 115 1 17 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 MET A 209 1 21 HELIX 10 10 VAL A 233 HIS A 256 1 24 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 GLY A 321 TYR A 331 1 11 HELIX 14 14 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 10 LEU A 63 PRO A 64 VAL A 67 MET A 122 SITE 2 AC1 10 GLY A 125 VAL A 126 TYR A 129 ASN A 142 SITE 3 AC1 10 ILE A 143 LEU A 147 SITE 1 AC2 1 LEU A 338 SITE 1 AC3 12 LYS A 246 ASN A 247 ARG A 250 ALA A 251 SITE 2 AC3 12 GLU A 254 ASP A 282 GLY A 284 GLY A 286 SITE 3 AC3 12 VAL A 287 THR A 346 HOH A2029 HOH A2039 CRYST1 108.944 108.944 84.380 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 0.009179 0.005300 0.000000 0.00000 SCALE2 0.000000 0.010599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011851 0.00000