HEADER OXIDOREDUCTASE/INHIBITOR 25-FEB-19 6O2Z TITLE CRYSTAL STRUCTURE OF IDH1 R132H MUTANT IN COMPLEX WITH COMPOUND 32 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDH,CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE,IDP,NADP(+)- COMPND 5 SPECIFIC ICDH,OXALOSUCCINATE DECARBOXYLASE; COMPND 6 EC: 1.1.1.42; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IDH1, PICD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3) KEYWDS IDH1, ALLOSTERIC INHIBITOR, OXIDOREDUCTASE, INHIBITOR COMPLEX, KEYWDS 2 OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.V.TOMS,J.LIN REVDAT 3 13-MAR-24 6O2Z 1 REMARK REVDAT 2 07-AUG-19 6O2Z 1 JRNL REVDAT 1 26-JUN-19 6O2Z 0 JRNL AUTH J.LIN,W.LU,J.A.CARAVELLA,A.M.CAMPBELL,R.B.DIEBOLD, JRNL AUTH 2 A.ERICSSON,E.FRITZEN,G.R.GUSTAFSON,D.R.LANCIA JR., JRNL AUTH 3 T.SHELEKHIN,Z.WANG,J.CASTRO,A.CLARKE,D.GOTUR,H.R.JOSEPHINE, JRNL AUTH 4 M.KATZ,H.DIEP,M.KERSHAW,L.YAO,G.KAUFFMAN,S.E.HUBBS,G.P.LUKE, JRNL AUTH 5 A.V.TOMS,L.WANG,K.W.BAIR,K.J.BARR,C.DINSMORE,D.WALKER, JRNL AUTH 6 S.ASHWELL JRNL TITL DISCOVERY AND OPTIMIZATION OF QUINOLINONE DERIVATIVES AS JRNL TITL 2 POTENT, SELECTIVE, AND ORALLY BIOAVAILABLE MUTANT ISOCITRATE JRNL TITL 3 DEHYDROGENASE 1 (MIDH1) INHIBITORS. JRNL REF J.MED.CHEM. V. 62 6575 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31199148 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00362 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 35493 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1894 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2530 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 135 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6480 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 154 REMARK 3 SOLVENT ATOMS : 140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.77000 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): 0.393 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.259 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.188 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.532 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6778 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6174 ; 0.002 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9165 ; 1.537 ; 1.655 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14366 ; 1.274 ; 1.587 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 818 ; 7.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;35.544 ;23.735 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1183 ;20.261 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;23.091 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 886 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7504 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1379 ; 0.002 ; 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): 3284 ; 3.348 ; 4.466 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3283 ; 3.334 ; 4.464 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4100 ; 4.975 ; 6.687 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4100 ; 4.976 ; 6.691 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3494 ; 4.222 ; 5.008 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3495 ; 4.221 ; 5.009 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5066 ; 6.551 ; 7.298 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7446 ; 8.303 ;51.324 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7437 ; 8.301 ;51.317 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 : NULL 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 6O2Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0750 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 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) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M TRI-AMMONIUM CITRATE PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 151.87000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.17200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.17200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 227.80500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.17200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.17200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.93500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.17200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.17200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 227.80500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.17200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.17200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.93500 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 151.87000 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: 8500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL 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 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 1 REMARK 465 SER A 2 REMARK 465 TYR A 135 REMARK 465 GLY A 136 REMARK 465 LEU A 416 REMARK 465 GLU A 417 REMARK 465 HIS A 418 REMARK 465 HIS A 419 REMARK 465 HIS A 420 REMARK 465 HIS A 421 REMARK 465 HIS A 422 REMARK 465 HIS A 423 REMARK 465 HIS A 424 REMARK 465 HIS A 425 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 TYR B 135 REMARK 465 GLY B 136 REMARK 465 LEU B 416 REMARK 465 GLU B 417 REMARK 465 HIS B 418 REMARK 465 HIS B 419 REMARK 465 HIS B 420 REMARK 465 HIS B 421 REMARK 465 HIS B 422 REMARK 465 HIS B 423 REMARK 465 HIS B 424 REMARK 465 HIS B 425 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 LYS A 3 CG CD CE NZ REMARK 470 LYS A 233 CG CD CE NZ REMARK 470 LYS A 350 CG CD CE NZ REMARK 470 LYS B 3 CG CD CE NZ REMARK 470 LYS B 87 CG CD CE NZ REMARK 470 ARG B 140 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 350 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP B 137 O HOH B 601 2.12 REMARK 500 NZ LYS B 29 OD1 ASP B 399 2.13 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 GLU A 17 -132.77 61.14 REMARK 500 ILE A 31 -61.84 -97.55 REMARK 500 ASN A 68 -12.25 83.98 REMARK 500 SER A 94 124.67 -37.29 REMARK 500 HIS A 133 -74.10 -69.28 REMARK 500 ARG A 140 58.84 -119.83 REMARK 500 PRO A 149 151.04 -42.94 REMARK 500 HIS A 170 139.39 -174.32 REMARK 500 LEU A 414 20.85 -143.87 REMARK 500 GLU B 17 -133.37 55.05 REMARK 500 ILE B 31 -68.26 -99.00 REMARK 500 ASP B 38 80.99 -69.60 REMARK 500 ASN B 68 -12.22 84.89 REMARK 500 LYS B 212 54.95 -112.67 REMARK 500 ASN B 271 97.34 -173.96 REMARK 500 ASP B 273 2.16 -62.04 REMARK 500 ALA B 412 35.77 -89.47 REMARK 500 LYS B 413 24.03 -141.88 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 B 273 GLY B 274 -148.19 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 LJV A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LJV B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 502 DBREF 6O2Z A 1 414 UNP O75874 IDHC_HUMAN 1 414 DBREF 6O2Z B 1 414 UNP O75874 IDHC_HUMAN 1 414 SEQADV 6O2Z HIS A 132 UNP O75874 ARG 132 ENGINEERED MUTATION SEQADV 6O2Z SER A 415 UNP O75874 EXPRESSION TAG SEQADV 6O2Z LEU A 416 UNP O75874 EXPRESSION TAG SEQADV 6O2Z GLU A 417 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 418 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 419 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 420 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 421 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 422 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 423 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 424 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS A 425 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 132 UNP O75874 ARG 132 ENGINEERED MUTATION SEQADV 6O2Z SER B 415 UNP O75874 EXPRESSION TAG SEQADV 6O2Z LEU B 416 UNP O75874 EXPRESSION TAG SEQADV 6O2Z GLU B 417 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 418 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 419 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 420 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 421 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 422 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 423 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 424 UNP O75874 EXPRESSION TAG SEQADV 6O2Z HIS B 425 UNP O75874 EXPRESSION TAG SEQRES 1 A 425 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 A 425 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 A 425 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 A 425 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 A 425 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 A 425 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 425 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 A 425 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 A 425 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 A 425 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 A 425 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 A 425 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 A 425 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 A 425 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 A 425 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 A 425 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 A 425 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 A 425 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 A 425 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 A 425 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 A 425 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 A 425 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 A 425 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 A 425 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 A 425 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 A 425 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 A 425 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 A 425 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 A 425 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 A 425 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 A 425 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 A 425 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU SER LEU SEQRES 33 A 425 GLU HIS HIS HIS HIS HIS HIS HIS HIS SEQRES 1 B 425 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 B 425 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 B 425 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 B 425 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 B 425 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 B 425 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 B 425 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 B 425 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 B 425 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 B 425 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 B 425 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 B 425 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 B 425 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 B 425 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 B 425 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 B 425 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 B 425 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 B 425 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 B 425 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 B 425 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 B 425 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 B 425 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 B 425 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 B 425 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 B 425 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 B 425 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 B 425 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 B 425 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 B 425 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 B 425 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 B 425 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 B 425 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU SER LEU SEQRES 33 B 425 GLU HIS HIS HIS HIS HIS HIS HIS HIS HET LJV A 500 23 HET NAP A 501 48 HET GOL A 502 6 HET LJV B 500 23 HET NAP B 501 48 HET GOL B 502 6 HETNAM LJV 6-{[(6-CHLORO-2-OXO-1,2-DIHYDROQUINOLIN-3-YL) HETNAM 2 LJV METHYL]AMINO}-2-METHYLPYRIDINE-3-CARBONITRILE HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM GOL GLYCEROL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 LJV 2(C17 H13 CL N4 O) FORMUL 4 NAP 2(C21 H28 N7 O17 P3) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 9 HOH *140(H2 O) HELIX 1 AA1 ASP A 16 ILE A 31 1 16 HELIX 2 AA2 GLY A 45 THR A 52 1 8 HELIX 3 AA3 ASP A 54 ASN A 68 1 15 HELIX 4 AA4 ASP A 79 LYS A 87 1 9 HELIX 5 AA5 SER A 94 GLY A 104 1 11 HELIX 6 AA6 ASP A 137 TYR A 139 5 3 HELIX 7 AA7 ASP A 186 GLY A 204 1 19 HELIX 8 AA8 LYS A 218 TYR A 235 1 18 HELIX 9 AA9 TYR A 235 ALA A 241 1 7 HELIX 10 AB1 ILE A 251 SER A 261 1 11 HELIX 11 AB2 ASP A 279 GLY A 284 1 6 HELIX 12 AB3 SER A 287 GLY A 289 5 3 HELIX 13 AB4 VAL A 312 LYS A 321 1 10 HELIX 14 AB5 PRO A 329 ASP A 347 1 19 HELIX 15 AB6 ASN A 349 ALA A 369 1 21 HELIX 16 AB7 THR A 373 GLY A 382 1 10 HELIX 17 AB8 LEU A 383 VAL A 386 5 4 HELIX 18 AB9 GLN A 387 TYR A 391 5 5 HELIX 19 AC1 ASN A 393 LYS A 413 1 21 HELIX 20 AC2 ASP B 16 LEU B 30 1 15 HELIX 21 AC3 GLY B 45 THR B 52 1 8 HELIX 22 AC4 ASP B 54 ASN B 68 1 15 HELIX 23 AC5 ASP B 79 LYS B 87 1 9 HELIX 24 AC6 SER B 94 GLY B 104 1 11 HELIX 25 AC7 ASP B 186 GLY B 204 1 19 HELIX 26 AC8 LYS B 218 TYR B 235 1 18 HELIX 27 AC9 TYR B 235 GLN B 242 1 8 HELIX 28 AD1 ILE B 251 LYS B 260 1 10 HELIX 29 AD2 ASP B 275 SER B 278 5 4 HELIX 30 AD3 ASP B 279 SER B 287 1 9 HELIX 31 AD4 VAL B 312 LYS B 321 1 10 HELIX 32 AD5 PRO B 329 ASN B 348 1 20 HELIX 33 AD6 ASN B 349 ALA B 369 1 21 HELIX 34 AD7 THR B 373 GLY B 382 1 10 HELIX 35 AD8 LEU B 383 VAL B 386 5 4 HELIX 36 AD9 GLN B 387 TYR B 391 5 5 HELIX 37 AE1 ASN B 393 GLN B 411 1 19 SHEET 1 AA110 VAL A 35 ASP A 43 0 SHEET 2 AA110 ILE A 5 GLN A 14 1 N ILE A 5 O GLU A 36 SHEET 3 AA110 VAL A 69 LYS A 72 1 O VAL A 69 N VAL A 11 SHEET 4 AA110 VAL A 303 ALA A 307 1 O ALA A 305 N LYS A 72 SHEET 5 AA110 MET A 291 VAL A 296 -1 N LEU A 295 O GLU A 304 SHEET 6 AA110 THR A 106 ALA A 111 -1 N PHE A 108 O VAL A 294 SHEET 7 AA110 ILE A 128 HIS A 132 -1 O ILE A 130 N ARG A 109 SHEET 8 AA110 PHE A 265 CYS A 269 1 O TRP A 267 N ILE A 129 SHEET 9 AA110 LEU A 207 THR A 211 1 N TYR A 208 O ALA A 268 SHEET 10 AA110 TYR A 246 LEU A 250 1 O ARG A 249 N LEU A 209 SHEET 1 AA2 4 ALA A 141 VAL A 146 0 SHEET 2 AA2 4 GLY A 177 GLN A 185 -1 O GLY A 177 N VAL A 146 SHEET 3 AA2 4 GLY B 177 GLN B 185 -1 O ASN B 184 N VAL A 178 SHEET 4 AA2 4 THR B 142 VAL B 146 -1 N VAL B 146 O GLY B 177 SHEET 1 AA3 4 VAL A 165 PHE A 172 0 SHEET 2 AA3 4 GLY A 150 PRO A 158 -1 N ILE A 154 O TYR A 167 SHEET 3 AA3 4 GLY B 150 PRO B 158 -1 O GLU B 153 N THR A 155 SHEET 4 AA3 4 VAL B 165 PHE B 172 -1 O TYR B 167 N ILE B 154 SHEET 1 AA410 VAL B 35 ASP B 43 0 SHEET 2 AA410 ILE B 5 GLN B 14 1 N ILE B 5 O GLU B 36 SHEET 3 AA410 VAL B 69 LYS B 72 1 O VAL B 69 N VAL B 11 SHEET 4 AA410 VAL B 303 ALA B 307 1 O ALA B 305 N LYS B 72 SHEET 5 AA410 MET B 291 VAL B 296 -1 N LEU B 295 O GLU B 304 SHEET 6 AA410 THR B 106 ALA B 111 -1 N PHE B 108 O VAL B 294 SHEET 7 AA410 ILE B 128 HIS B 133 -1 O HIS B 132 N VAL B 107 SHEET 8 AA410 PHE B 265 CYS B 269 1 O TRP B 267 N ILE B 129 SHEET 9 AA410 LEU B 207 THR B 211 1 N TYR B 208 O ILE B 266 SHEET 10 AA410 TYR B 246 LEU B 250 1 O ARG B 249 N LEU B 209 SITE 1 AC1 14 ARG A 109 ALA A 111 ILE A 113 ARG A 119 SITE 2 AC1 14 LEU A 120 TRP A 124 ILE A 128 ILE A 130 SITE 3 AC1 14 TRP A 267 ASP A 279 VAL A 281 TYR A 285 SITE 4 AC1 14 HOH A 651 SER B 280 SITE 1 AC2 21 LYS A 72 ALA A 74 THR A 75 ILE A 76 SITE 2 AC2 21 THR A 77 ARG A 82 ASN A 96 GLY A 289 SITE 3 AC2 21 GLU A 306 HIS A 309 GLY A 310 THR A 311 SITE 4 AC2 21 VAL A 312 THR A 313 ARG A 314 HIS A 315 SITE 5 AC2 21 ASN A 328 HOH A 604 HOH A 607 HOH A 608 SITE 6 AC2 21 HOH A 640 SITE 1 AC3 6 SER A 6 GLY A 7 GLY A 8 GLU A 36 SITE 2 AC3 6 ASP A 38 ASN B 53 SITE 1 AC4 16 SER A 280 ARG B 109 ALA B 111 ILE B 113 SITE 2 AC4 16 ARG B 119 LEU B 120 TRP B 124 ILE B 128 SITE 3 AC4 16 ILE B 130 MET B 259 TRP B 267 ASP B 279 SITE 4 AC4 16 VAL B 281 ALA B 282 TYR B 285 HOH B 641 SITE 1 AC5 20 LYS B 72 THR B 75 THR B 77 ARG B 82 SITE 2 AC5 20 ASN B 96 SER B 287 GLU B 306 HIS B 309 SITE 3 AC5 20 GLY B 310 THR B 311 VAL B 312 THR B 313 SITE 4 AC5 20 ARG B 314 HIS B 315 ASN B 328 ASP B 375 SITE 5 AC5 20 HOH B 616 HOH B 630 HOH B 634 HOH B 640 SITE 1 AC6 4 SER B 6 GLY B 8 GLU B 36 ASP B 38 CRYST1 82.344 82.344 303.740 90.00 90.00 90.00 P 43 21 2 16 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 0.012144 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012144 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003292 0.00000