HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 26-NOV-12 4I3L TITLE CRYSTAL STRUCTURE OF A METABOLIC REDUCTASE WITH 6-BENZYL-1-HYDROXY-4- TITLE 2 METHYLPYRIDIN-2(1H)-ONE 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: 469008 KEYWDS ISOCITRATE DEHYDROGENASE, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.ZHENG,Y.YAO,Z.LIU,L.DENG,J.L.ANGLIN,H.JIANG,B.V.V.PRASAD,Y.SONG REVDAT 3 28-FEB-24 4I3L 1 REMARK SEQADV REVDAT 2 10-JUL-13 4I3L 1 JRNL REVDAT 1 22-MAY-13 4I3L 0 JRNL AUTH B.ZHENG,Y.YAO,Z.LIU,L.DENG,J.L.ANGLIN,H.JIANG,B.V.PRASAD, JRNL AUTH 2 Y.SONG JRNL TITL CRYSTALLOGRAPHIC INVESTIGATION AND SELECTIVE INHIBITION OF JRNL TITL 2 MUTANT ISOCITRATE DEHYDROGENASE. JRNL REF ACS MED CHEM LETT V. 4 542 2013 JRNL REFN ISSN 1948-5875 JRNL PMID 23795241 JRNL DOI 10.1021/ML400036Z REMARK 2 REMARK 2 RESOLUTION. 3.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 3.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 14772 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 774 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) : 3.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.38 REMARK 3 REFLECTION IN BIN (WORKING SET) : 850 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2770 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.4000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 122 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.13000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.628 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.470 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.678 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.888 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.780 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6011 ; 0.009 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8114 ; 1.423 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 713 ; 6.343 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 272 ;40.184 ;24.890 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1072 ;20.214 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;20.551 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 883 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4434 ; 0.005 ; 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4I3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076260. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.7 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15547 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.290 REMARK 200 RESOLUTION RANGE LOW (A) : 45.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM NADPH AND 10 MM CACL2 IN A REMARK 280 SOLUTION OF 1.75 M (NH4)2SO4 AND 0.1 M NAAC (PH 5.7), VAPOR REMARK 280 DIFFUSION, HANGING 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 152.41800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 40.42650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 40.42650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 228.62700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 40.42650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 40.42650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.20900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 40.42650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.42650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 228.62700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 40.42650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.42650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.20900 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 152.41800 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: 6570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 LYS A 3 REMARK 465 ILE A 117 REMARK 465 PRO A 118 REMARK 465 ARG A 119 REMARK 465 LEU A 120 REMARK 465 VAL A 121 REMARK 465 SER A 122 REMARK 465 GLY A 123 REMARK 465 TRP A 124 REMARK 465 VAL A 125 REMARK 465 LYS A 126 REMARK 465 ALA A 134 REMARK 465 TYR A 135 REMARK 465 GLY A 136 REMARK 465 ASP A 137 REMARK 465 GLN A 138 REMARK 465 TYR A 139 REMARK 465 ARG A 140 REMARK 465 ALA A 256 REMARK 465 GLN A 257 REMARK 465 ALA A 258 REMARK 465 MET A 259 REMARK 465 LYS A 260 REMARK 465 SER A 261 REMARK 465 GLU A 262 REMARK 465 GLY A 263 REMARK 465 TYR A 272 REMARK 465 ASP A 273 REMARK 465 GLY A 274 REMARK 465 ASP A 275 REMARK 465 VAL A 276 REMARK 465 GLN A 277 REMARK 465 SER A 278 REMARK 465 ASP A 279 REMARK 465 SER A 280 REMARK 465 VAL A 281 REMARK 465 ALA A 282 REMARK 465 GLN A 283 REMARK 465 GLY A 284 REMARK 465 TYR A 285 REMARK 465 GLY A 286 REMARK 465 SER A 287 REMARK 465 ALA A 412 REMARK 465 LYS A 413 REMARK 465 LEU A 414 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 LYS B 3 REMARK 465 ARG B 119 REMARK 465 LEU B 120 REMARK 465 VAL B 121 REMARK 465 SER B 122 REMARK 465 GLY B 123 REMARK 465 TRP B 124 REMARK 465 VAL B 125 REMARK 465 LYS B 126 REMARK 465 ALA B 134 REMARK 465 TYR B 135 REMARK 465 GLY B 136 REMARK 465 ASP B 137 REMARK 465 GLN B 138 REMARK 465 TYR B 139 REMARK 465 ARG B 140 REMARK 465 THR B 211 REMARK 465 LYS B 212 REMARK 465 ASN B 213 REMARK 465 THR B 214 REMARK 465 ILE B 215 REMARK 465 LYS B 236 REMARK 465 SER B 237 REMARK 465 GLN B 238 REMARK 465 PHE B 239 REMARK 465 GLU B 240 REMARK 465 ALA B 241 REMARK 465 VAL B 255 REMARK 465 ALA B 256 REMARK 465 GLN B 257 REMARK 465 ALA B 258 REMARK 465 MET B 259 REMARK 465 LYS B 260 REMARK 465 SER B 261 REMARK 465 LYS B 270 REMARK 465 ASN B 271 REMARK 465 TYR B 272 REMARK 465 ASP B 273 REMARK 465 GLY B 274 REMARK 465 ASP B 275 REMARK 465 VAL B 276 REMARK 465 GLN B 277 REMARK 465 SER B 278 REMARK 465 ASP B 279 REMARK 465 SER B 280 REMARK 465 VAL B 281 REMARK 465 ALA B 282 REMARK 465 GLN B 283 REMARK 465 GLY B 284 REMARK 465 TYR B 285 REMARK 465 GLY B 286 REMARK 465 ALA B 412 REMARK 465 LYS B 413 REMARK 465 LEU B 414 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 -121.62 51.90 REMARK 500 ILE A 31 -63.98 -100.73 REMARK 500 ASN A 68 -12.09 83.55 REMARK 500 GLU A 80 -37.84 -35.66 REMARK 500 HIS A 132 -140.50 -73.32 REMARK 500 THR A 162 -178.03 -58.84 REMARK 500 HIS A 170 150.55 179.88 REMARK 500 GLU A 174 -107.26 -94.15 REMARK 500 ASN A 184 140.67 178.40 REMARK 500 LYS A 212 64.44 -102.03 REMARK 500 TYR A 219 -77.12 -68.52 REMARK 500 ALA A 241 8.82 -59.53 REMARK 500 MET A 254 -70.83 -66.56 REMARK 500 HIS A 309 -179.73 -66.17 REMARK 500 SER A 326 55.58 -147.01 REMARK 500 GLU A 368 -1.74 -55.12 REMARK 500 GLU B 17 -140.83 44.52 REMARK 500 ILE B 31 -73.68 -93.57 REMARK 500 TYR B 34 -21.66 -147.51 REMARK 500 ASN B 53 74.47 44.46 REMARK 500 ASP B 54 27.13 33.74 REMARK 500 ASN B 68 -11.81 90.77 REMARK 500 PRO B 158 163.08 -39.66 REMARK 500 ASP B 160 30.33 -93.76 REMARK 500 LYS B 164 38.82 -157.55 REMARK 500 HIS B 170 149.28 -170.19 REMARK 500 GLU B 173 -42.80 -141.05 REMARK 500 GLU B 174 -78.90 -33.66 REMARK 500 LYS B 217 -80.45 -38.98 REMARK 500 TYR B 219 -80.64 -95.42 REMARK 500 ASP B 220 -25.16 -33.33 REMARK 500 ASP B 232 30.85 -90.68 REMARK 500 LYS B 233 -27.47 -155.10 REMARK 500 GLU B 247 -155.70 -145.82 REMARK 500 ILE B 251 -53.74 -29.18 REMARK 500 SER B 326 81.20 -155.65 REMARK 500 ALA B 369 0.64 -65.36 REMARK 500 ILE B 380 -79.04 -63.34 REMARK 500 ASN B 385 62.03 -110.76 REMARK 500 SER B 389 1.62 -68.93 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 NDP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1BZ A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NDP B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MAP RELATED DB: PDB DBREF 4I3L A 1 414 UNP O75874 IDHC_HUMAN 1 414 DBREF 4I3L B 1 414 UNP O75874 IDHC_HUMAN 1 414 SEQADV 4I3L HIS A 132 UNP O75874 ARG 132 ENGINEERED MUTATION SEQADV 4I3L HIS B 132 UNP O75874 ARG 132 ENGINEERED MUTATION SEQRES 1 A 414 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 A 414 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 A 414 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 A 414 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 A 414 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 A 414 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 414 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 A 414 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 A 414 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 A 414 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 A 414 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 A 414 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 A 414 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 A 414 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 A 414 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 A 414 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 A 414 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 A 414 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 A 414 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 A 414 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 A 414 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 A 414 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 A 414 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 A 414 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 A 414 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 A 414 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 A 414 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 A 414 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 A 414 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 A 414 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 A 414 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 A 414 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU SEQRES 1 B 414 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 B 414 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 B 414 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 B 414 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 B 414 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 B 414 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 B 414 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 B 414 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 B 414 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 B 414 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 B 414 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 B 414 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 B 414 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 B 414 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 B 414 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 B 414 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 B 414 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 B 414 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 B 414 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 B 414 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 B 414 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 B 414 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 B 414 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 B 414 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 B 414 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 B 414 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 B 414 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 B 414 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 B 414 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 B 414 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 B 414 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 B 414 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU HET NDP A 501 48 HET SO4 A 502 5 HET SO4 A 503 5 HET 1BZ A 504 16 HET NDP B 501 48 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM SO4 SULFATE ION HETNAM 1BZ 6-BENZYL-1-HYDROXY-4-METHYLPYRIDIN-2(1H)-ONE FORMUL 3 NDP 2(C21 H30 N7 O17 P3) FORMUL 4 SO4 2(O4 S 2-) FORMUL 6 1BZ C13 H13 N O2 HELIX 1 1 ASP A 16 ILE A 31 1 16 HELIX 2 2 GLY A 45 THR A 52 1 8 HELIX 3 3 ASP A 54 ASN A 68 1 15 HELIX 4 4 ASP A 79 LYS A 87 1 9 HELIX 5 5 SER A 94 GLY A 104 1 11 HELIX 6 6 ASP A 186 GLY A 204 1 19 HELIX 7 7 TYR A 219 TYR A 235 1 17 HELIX 8 8 TYR A 235 ALA A 241 1 7 HELIX 9 9 ILE A 251 VAL A 255 1 5 HELIX 10 10 VAL A 312 LYS A 321 1 10 HELIX 11 11 PRO A 329 ASP A 347 1 19 HELIX 12 12 ASN A 349 GLU A 368 1 20 HELIX 13 13 THR A 373 GLY A 382 1 10 HELIX 14 14 LEU A 383 VAL A 386 5 4 HELIX 15 15 GLN A 387 TYR A 391 5 5 HELIX 16 16 ASN A 393 GLN A 411 1 19 HELIX 17 17 ASP B 16 ILE B 31 1 16 HELIX 18 18 GLY B 45 THR B 52 1 8 HELIX 19 19 ASP B 54 ASN B 68 1 15 HELIX 20 20 ASP B 79 PHE B 86 1 8 HELIX 21 21 SER B 94 GLY B 104 1 11 HELIX 22 22 ASP B 186 LYS B 203 1 18 HELIX 23 23 LYS B 217 TYR B 235 1 19 HELIX 24 24 LEU B 250 MET B 254 5 5 HELIX 25 25 VAL B 312 GLY B 322 1 11 HELIX 26 26 PRO B 329 ASN B 348 1 20 HELIX 27 27 ASN B 349 ALA B 369 1 21 HELIX 28 28 THR B 373 GLY B 382 1 10 HELIX 29 29 LEU B 383 VAL B 386 5 4 HELIX 30 30 GLN B 387 TYR B 391 5 5 HELIX 31 31 ASN B 393 GLN B 411 1 19 SHEET 1 A10 VAL A 35 ASP A 43 0 SHEET 2 A10 ILE A 5 GLN A 14 1 N GLY A 7 O GLU A 36 SHEET 3 A10 VAL A 69 LYS A 72 1 O VAL A 69 N VAL A 11 SHEET 4 A10 VAL A 303 ALA A 307 1 O ALA A 305 N GLY A 70 SHEET 5 A10 MET A 291 VAL A 296 -1 N LEU A 295 O GLU A 304 SHEET 6 A10 ARG A 109 ALA A 111 -1 N GLU A 110 O THR A 292 SHEET 7 A10 ILE A 128 GLY A 131 -1 O ILE A 130 N ARG A 109 SHEET 8 A10 PHE A 265 CYS A 269 1 O TRP A 267 N ILE A 129 SHEET 9 A10 LEU A 207 THR A 211 1 N TYR A 208 O ALA A 268 SHEET 10 A10 TYR A 246 LEU A 250 1 O ARG A 249 N LEU A 209 SHEET 1 B 4 THR A 142 VAL A 146 0 SHEET 2 B 4 GLY A 177 GLN A 185 -1 O GLY A 177 N VAL A 146 SHEET 3 B 4 GLY B 177 GLN B 185 -1 O MET B 182 N MET A 180 SHEET 4 B 4 THR B 142 VAL B 146 -1 N VAL B 146 O GLY B 177 SHEET 1 C 4 VAL A 165 PHE A 172 0 SHEET 2 C 4 GLY A 150 PRO A 158 -1 N ILE A 154 O TYR A 167 SHEET 3 C 4 GLY B 150 PRO B 158 -1 O THR B 157 N LYS A 151 SHEET 4 C 4 THR B 166 PHE B 172 -1 O VAL B 169 N VAL B 152 SHEET 1 D 9 VAL B 35 ASP B 43 0 SHEET 2 D 9 ILE B 5 GLN B 14 1 N ILE B 5 O GLU B 36 SHEET 3 D 9 VAL B 69 LYS B 72 1 O VAL B 71 N VAL B 11 SHEET 4 D 9 VAL B 303 ALA B 307 1 O ALA B 305 N GLY B 70 SHEET 5 D 9 MET B 291 VAL B 296 -1 N LEU B 295 O GLU B 304 SHEET 6 D 9 THR B 106 ALA B 111 -1 N THR B 106 O VAL B 296 SHEET 7 D 9 ILE B 128 GLY B 131 -1 O ILE B 130 N ARG B 109 SHEET 8 D 9 PHE B 265 ALA B 268 1 O TRP B 267 N ILE B 129 SHEET 9 D 9 LEU B 207 LEU B 209 1 N TYR B 208 O ALA B 268 SITE 1 AC1 17 LYS A 72 ALA A 74 THR A 75 THR A 77 SITE 2 AC1 17 ARG A 82 LEU A 288 GLU A 306 HIS A 309 SITE 3 AC1 17 GLY A 310 THR A 311 VAL A 312 THR A 313 SITE 4 AC1 17 ARG A 314 HIS A 315 THR A 327 ASN A 328 SITE 5 AC1 17 1BZ A 504 SITE 1 AC2 2 ARG A 314 LYS A 374 SITE 1 AC3 7 HIS A 170 ASN A 171 PHE A 172 GLU A 173 SITE 2 AC3 7 GLU A 174 GLY A 175 GLN B 185 SITE 1 AC4 2 ARG A 100 NDP A 501 SITE 1 AC5 17 LYS B 72 ALA B 74 THR B 75 THR B 77 SITE 2 AC5 17 ARG B 82 ASN B 96 LEU B 288 GLU B 306 SITE 3 AC5 17 HIS B 309 GLY B 310 THR B 311 VAL B 312 SITE 4 AC5 17 THR B 313 ARG B 314 HIS B 315 THR B 327 SITE 5 AC5 17 ASN B 328 CRYST1 80.853 80.853 304.836 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 0.012368 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012368 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003280 0.00000