PDB Short entry for 3MAS HEADER OXIDOREDUCTASE 24-MAR-10 3MAS TITLE CRYSTAL STRUCTURE OF HETERODIMERIC R132H MUTANT OF HUMAN CYTOSOLIC TITLE 2 NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH NADP AND TITLE 3 ISOCITRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IDH, CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE, OXALOSUCCINATE COMPND 5 DECARBOXYLASE, NADP(+)-SPECIFIC ICDH, IDP; COMPND 6 EC: 1.1.1.42; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC; COMPND 11 CHAIN: B; COMPND 12 SYNONYM: IDH, CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE, OXALOSUCCINATE COMPND 13 DECARBOXYLASE, NADP(+)-SPECIFIC ICDH, IDP; COMPND 14 EC: 1.1.1.42; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IDH1, PICD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: IDH1, PICD; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1 KEYWDS ISOCITRATE DEHYDROGENASE, NICOTINAMIDE ADENINE DINUCLEOTIDE KEYWDS 2 PHOSPHATE, ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.YANG,Y.PENG,J.DING REVDAT 5 01-NOV-23 3MAS 1 REMARK REVDAT 4 10-NOV-21 3MAS 1 REMARK SEQADV REVDAT 3 08-NOV-17 3MAS 1 REMARK REVDAT 2 21-MAY-14 3MAS 1 JRNL VERSN REVDAT 1 10-NOV-10 3MAS 0 JRNL AUTH B.YANG,C.ZHONG,Y.PENG,Z.LAI,J.DING JRNL TITL MOLECULAR MECHANISMS OF "OFF-ON SWITCH" OF ACTIVITIES OF JRNL TITL 2 HUMAN IDH1 BY TUMOR-ASSOCIATED MUTATION R132H. JRNL REF CELL RES. V. 20 1188 2010 JRNL REFN ISSN 1001-0602 JRNL PMID 20975740 JRNL DOI 10.1038/CR.2010.145 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.5_2 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 17148 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 871 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.5530 - 5.8130 0.90 2884 150 0.2260 0.2730 REMARK 3 2 5.8130 - 4.6150 0.92 2753 143 0.1990 0.2530 REMARK 3 3 4.6150 - 4.0320 0.91 2707 145 0.2020 0.2510 REMARK 3 4 4.0320 - 3.6630 0.94 2757 141 0.2320 0.2990 REMARK 3 5 3.6630 - 3.4010 0.91 2655 137 0.2650 0.3180 REMARK 3 6 3.4010 - 3.2000 0.88 2521 155 0.3040 0.3480 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 47.65 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.400 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 85.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.64400 REMARK 3 B22 (A**2) : -1.64400 REMARK 3 B33 (A**2) : 3.28700 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 6491 REMARK 3 ANGLE : 0.756 8762 REMARK 3 CHIRALITY : 0.057 957 REMARK 3 PLANARITY : 0.012 1103 REMARK 3 DIHEDRAL : 19.744 2499 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3MAS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058321. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18264 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 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 (%) : 96.8 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 0.59600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1T09 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NA, 2% PEG 400, 2.0M REMARK 280 (NH4)2SO4, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 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 154.25400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.56800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.56800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 231.38100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.56800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.56800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 77.12700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.56800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.56800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 231.38100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.56800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.56800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 77.12700 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 154.25400 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 ASP A 137 REMARK 465 GLN A 138 REMARK 465 TYR A 139 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 LEU A 415 REMARK 465 GLU A 416 REMARK 465 HIS 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 GLY B -4 REMARK 465 SER B -3 REMARK 465 PRO B -2 REMARK 465 GLU B -1 REMARK 465 PHE B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 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 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 LEU B 414 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 O THR A 75 N7N NAP A 423 2.03 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 LYS A 4 154.33 -38.60 REMARK 500 GLU A 17 -141.49 48.21 REMARK 500 ASP A 38 88.75 -67.11 REMARK 500 ASP A 54 -0.34 66.13 REMARK 500 ASN A 68 -17.13 72.24 REMARK 500 LYS A 89 -6.85 -59.21 REMARK 500 PRO A 118 97.78 -51.20 REMARK 500 VAL A 121 117.02 -161.14 REMARK 500 SER A 122 3.63 -67.05 REMARK 500 GLU A 174 -89.87 -121.58 REMARK 500 ASN A 184 114.42 -179.22 REMARK 500 ILE A 215 -70.34 -83.40 REMARK 500 TYR A 219 -75.81 -72.00 REMARK 500 TYR A 235 -8.43 81.69 REMARK 500 LYS A 260 45.79 -82.96 REMARK 500 GLU A 368 7.49 -69.21 REMARK 500 ASN A 393 -161.64 -69.50 REMARK 500 GLU B 17 -137.27 51.93 REMARK 500 ILE B 31 -62.28 -99.02 REMARK 500 ASP B 54 22.74 49.65 REMARK 500 ASN B 68 -17.87 75.40 REMARK 500 ASP B 79 -159.71 -121.46 REMARK 500 GLN B 90 152.84 166.77 REMARK 500 SER B 122 -5.83 -59.61 REMARK 500 PRO B 149 -159.47 -79.13 REMARK 500 ASP B 160 -43.29 -29.13 REMARK 500 THR B 162 -120.28 -70.30 REMARK 500 GLN B 163 173.58 -51.22 REMARK 500 HIS B 170 149.17 -176.00 REMARK 500 GLU B 173 -35.78 -132.18 REMARK 500 LYS B 212 63.58 -101.06 REMARK 500 LEU B 216 79.64 -105.29 REMARK 500 GLN B 234 -33.16 -137.90 REMARK 500 ILE B 244 -162.95 -114.81 REMARK 500 TRP B 245 165.11 178.19 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 NAP A 423 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 424 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT B 416 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MAP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HOMODIMERIC R132H MUTANT OF HUMAN CYTOSOLIC REMARK 900 NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH NADP AND REMARK 900 ISOCITRATE REMARK 900 RELATED ID: 3MAR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HOMODIMERIC R132H MUTANT OF HUMAN CYTOSOLIC REMARK 900 NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH NADP REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN IS A HETERODIMERIC MUTANT, WITH ARG 132 MUTATED TO HIS REMARK 999 132 IN ONE SUBUNIT, WHILE THE ARG132 IN THE OTHER SUBUNIT REMAINED REMARK 999 THE SAME AS WILD TYPE PROTEIN DBREF 3MAS A 1 414 UNP O75874 IDHC_HUMAN 1 414 DBREF 3MAS B 1 414 UNP O75874 IDHC_HUMAN 1 414 SEQADV 3MAS HIS A 132 UNP O75874 ARG 132 ENGINEERED MUTATION SEQADV 3MAS LEU A 415 UNP O75874 EXPRESSION TAG SEQADV 3MAS GLU A 416 UNP O75874 EXPRESSION TAG SEQADV 3MAS HIS A 417 UNP O75874 EXPRESSION TAG SEQADV 3MAS HIS A 418 UNP O75874 EXPRESSION TAG SEQADV 3MAS HIS A 419 UNP O75874 EXPRESSION TAG SEQADV 3MAS HIS A 420 UNP O75874 EXPRESSION TAG SEQADV 3MAS HIS A 421 UNP O75874 EXPRESSION TAG SEQADV 3MAS HIS A 422 UNP O75874 EXPRESSION TAG SEQADV 3MAS GLY B -4 UNP O75874 EXPRESSION TAG SEQADV 3MAS SER B -3 UNP O75874 EXPRESSION TAG SEQADV 3MAS PRO B -2 UNP O75874 EXPRESSION TAG SEQADV 3MAS GLU B -1 UNP O75874 EXPRESSION TAG SEQADV 3MAS PHE B 0 UNP O75874 EXPRESSION TAG SEQRES 1 A 422 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 A 422 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 A 422 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 A 422 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 A 422 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 A 422 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 422 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 A 422 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 A 422 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 A 422 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 A 422 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 A 422 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 A 422 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 A 422 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 A 422 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 A 422 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 A 422 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 A 422 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 A 422 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 A 422 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 A 422 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 A 422 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 A 422 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 A 422 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 A 422 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 A 422 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 A 422 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 A 422 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 A 422 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 A 422 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 A 422 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 A 422 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU LEU GLU SEQRES 33 A 422 HIS HIS HIS HIS HIS HIS SEQRES 1 B 419 GLY SER PRO GLU PHE MET SER LYS LYS ILE SER GLY GLY SEQRES 2 B 419 SER VAL VAL GLU MET GLN GLY ASP GLU MET THR ARG ILE SEQRES 3 B 419 ILE TRP GLU LEU ILE LYS GLU LYS LEU ILE PHE PRO TYR SEQRES 4 B 419 VAL GLU LEU ASP LEU HIS SER TYR ASP LEU GLY ILE GLU SEQRES 5 B 419 ASN ARG ASP ALA THR ASN ASP GLN VAL THR LYS ASP ALA SEQRES 6 B 419 ALA GLU ALA ILE LYS LYS HIS ASN VAL GLY VAL LYS CYS SEQRES 7 B 419 ALA THR ILE THR PRO ASP GLU LYS ARG VAL GLU GLU PHE SEQRES 8 B 419 LYS LEU LYS GLN MET TRP LYS SER PRO ASN GLY THR ILE SEQRES 9 B 419 ARG ASN ILE LEU GLY GLY THR VAL PHE ARG GLU ALA ILE SEQRES 10 B 419 ILE CYS LYS ASN ILE PRO ARG LEU VAL SER GLY TRP VAL SEQRES 11 B 419 LYS PRO ILE ILE ILE GLY ARG HIS ALA TYR GLY ASP GLN SEQRES 12 B 419 TYR ARG ALA THR ASP PHE VAL VAL PRO GLY PRO GLY LYS SEQRES 13 B 419 VAL GLU ILE THR TYR THR PRO SER ASP GLY THR GLN LYS SEQRES 14 B 419 VAL THR TYR LEU VAL HIS ASN PHE GLU GLU GLY GLY GLY SEQRES 15 B 419 VAL ALA MET GLY MET TYR ASN GLN ASP LYS SER ILE GLU SEQRES 16 B 419 ASP PHE ALA HIS SER SER PHE GLN MET ALA LEU SER LYS SEQRES 17 B 419 GLY TRP PRO LEU TYR LEU SER THR LYS ASN THR ILE LEU SEQRES 18 B 419 LYS LYS TYR ASP GLY ARG PHE LYS ASP ILE PHE GLN GLU SEQRES 19 B 419 ILE TYR ASP LYS GLN TYR LYS SER GLN PHE GLU ALA GLN SEQRES 20 B 419 LYS ILE TRP TYR GLU HIS ARG LEU ILE ASP ASP MET VAL SEQRES 21 B 419 ALA GLN ALA MET LYS SER GLU GLY GLY PHE ILE TRP ALA SEQRES 22 B 419 CYS LYS ASN TYR ASP GLY ASP VAL GLN SER ASP SER VAL SEQRES 23 B 419 ALA GLN GLY TYR GLY SER LEU GLY MET MET THR SER VAL SEQRES 24 B 419 LEU VAL CYS PRO ASP GLY LYS THR VAL GLU ALA GLU ALA SEQRES 25 B 419 ALA HIS GLY THR VAL THR ARG HIS TYR ARG MET TYR GLN SEQRES 26 B 419 LYS GLY GLN GLU THR SER THR ASN PRO ILE ALA SER ILE SEQRES 27 B 419 PHE ALA TRP THR ARG GLY LEU ALA HIS ARG ALA LYS LEU SEQRES 28 B 419 ASP ASN ASN LYS GLU LEU ALA PHE PHE ALA ASN ALA LEU SEQRES 29 B 419 GLU GLU VAL SER ILE GLU THR ILE GLU ALA GLY PHE MET SEQRES 30 B 419 THR LYS ASP LEU ALA ALA CYS ILE LYS GLY LEU PRO ASN SEQRES 31 B 419 VAL GLN ARG SER ASP TYR LEU ASN THR PHE GLU PHE MET SEQRES 32 B 419 ASP LYS LEU GLY GLU ASN LEU LYS ILE LYS LEU ALA GLN SEQRES 33 B 419 ALA LYS LEU HET NAP A 423 48 HET ICT A 424 13 HET NAP B 415 48 HET ICT B 416 13 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM ICT ISOCITRIC ACID HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) FORMUL 4 ICT 2(C6 H8 O7) HELIX 1 1 ASP A 16 LEU A 30 1 15 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 LYS A 203 1 18 HELIX 7 7 LYS A 218 GLN A 234 1 17 HELIX 8 8 TYR A 235 ALA A 241 1 7 HELIX 9 9 ILE A 251 LYS A 260 1 10 HELIX 10 10 VAL A 312 LYS A 321 1 10 HELIX 11 11 PRO A 329 ASN A 348 1 20 HELIX 12 12 ASN A 349 GLU A 368 1 20 HELIX 13 13 THR A 373 VAL A 386 1 14 HELIX 14 14 GLN A 387 TYR A 391 5 5 HELIX 15 15 ASN A 393 LYS A 413 1 21 HELIX 16 16 ASP B 16 LEU B 30 1 15 HELIX 17 17 GLY B 45 THR B 52 1 8 HELIX 18 18 ASP B 54 ASN B 68 1 15 HELIX 19 19 ASP B 79 LYS B 87 1 9 HELIX 20 20 SER B 94 GLY B 104 1 11 HELIX 21 21 ASP B 186 LYS B 203 1 18 HELIX 22 22 LEU B 216 TYR B 235 1 20 HELIX 23 23 TYR B 235 GLN B 242 1 8 HELIX 24 24 ILE B 251 LYS B 260 1 10 HELIX 25 25 SER B 287 GLY B 289 5 3 HELIX 26 26 VAL B 312 GLY B 322 1 11 HELIX 27 27 PRO B 329 ASN B 348 1 20 HELIX 28 28 ASN B 349 ALA B 369 1 21 HELIX 29 29 THR B 373 GLY B 382 1 10 HELIX 30 30 LEU B 383 VAL B 386 5 4 HELIX 31 31 GLN B 387 TYR B 391 5 5 HELIX 32 32 ASN B 393 ALA B 412 1 20 SHEET 1 A 3 VAL A 35 LEU A 39 0 SHEET 2 A 3 ILE A 5 GLN A 14 1 N GLY A 7 O GLU A 36 SHEET 3 A 3 TYR A 42 ASP A 43 1 O TYR A 42 N GLU A 12 SHEET 1 B10 VAL A 35 LEU A 39 0 SHEET 2 B10 ILE A 5 GLN A 14 1 N GLY A 7 O GLU A 36 SHEET 3 B10 VAL A 69 LYS A 72 1 O VAL A 69 N VAL A 11 SHEET 4 B10 VAL A 303 ALA A 307 1 O ALA A 305 N GLY A 70 SHEET 5 B10 MET A 291 VAL A 296 -1 N LEU A 295 O GLU A 304 SHEET 6 B10 THR A 106 ALA A 111 -1 N PHE A 108 O VAL A 294 SHEET 7 B10 ILE A 128 ILE A 130 -1 O ILE A 130 N ARG A 109 SHEET 8 B10 PHE A 265 CYS A 269 1 O TRP A 267 N ILE A 129 SHEET 9 B10 LEU A 207 THR A 211 1 N TYR A 208 O ILE A 266 SHEET 10 B10 TYR A 246 LEU A 250 1 O GLU A 247 N LEU A 207 SHEET 1 C 4 THR A 142 VAL A 146 0 SHEET 2 C 4 GLY A 177 GLN A 185 -1 O GLY A 177 N VAL A 146 SHEET 3 C 4 GLY B 177 GLN B 185 -1 O MET B 180 N MET A 182 SHEET 4 C 4 THR B 142 VAL B 145 -1 N PHE B 144 O ALA B 179 SHEET 1 D 4 VAL A 165 PHE A 172 0 SHEET 2 D 4 GLY A 150 PRO A 158 -1 N TYR A 156 O VAL A 165 SHEET 3 D 4 GLY B 150 PRO B 158 -1 O THR B 157 N LYS A 151 SHEET 4 D 4 VAL B 165 PHE B 172 -1 O TYR B 167 N ILE B 154 SHEET 1 E 6 VAL B 35 ASP B 43 0 SHEET 2 E 6 ILE B 5 GLN B 14 1 N GLU B 12 O TYR B 42 SHEET 3 E 6 VAL B 69 LYS B 72 1 O VAL B 71 N MET B 13 SHEET 4 E 6 VAL B 303 ALA B 307 1 O ALA B 305 N LYS B 72 SHEET 5 E 6 MET B 291 VAL B 296 -1 N LEU B 295 O GLU B 304 SHEET 6 E 6 THR B 106 ALA B 111 -1 N THR B 106 O VAL B 296 SHEET 1 F 4 LYS B 126 ARG B 132 0 SHEET 2 F 4 GLY B 263 CYS B 269 1 O TRP B 267 N ILE B 129 SHEET 3 F 4 LEU B 207 THR B 211 1 N TYR B 208 O ALA B 268 SHEET 4 F 4 TYR B 246 LEU B 250 1 O ARG B 249 N LEU B 209 CISPEP 1 GLY B 148 PRO B 149 0 -1.01 SITE 1 AC1 14 LYS A 72 THR A 75 THR A 77 ARG A 82 SITE 2 AC1 14 ASN A 96 GLY A 310 THR A 311 VAL A 312 SITE 3 AC1 14 THR A 313 ARG A 314 HIS A 315 THR A 327 SITE 4 AC1 14 ASN A 328 ICT A 424 SITE 1 AC2 16 LYS B 72 THR B 75 THR B 77 ARG B 82 SITE 2 AC2 16 ASN B 96 GLY B 289 HIS B 309 GLY B 310 SITE 3 AC2 16 THR B 311 VAL B 312 THR B 313 ARG B 314 SITE 4 AC2 16 HIS B 315 THR B 327 ASN B 328 ICT B 416 SITE 1 AC3 5 THR A 77 SER A 94 ASN A 96 ARG A 100 SITE 2 AC3 5 NAP A 423 SITE 1 AC4 5 THR B 77 SER B 94 ASN B 96 ARG B 100 SITE 2 AC4 5 NAP B 415 CRYST1 83.136 83.136 308.508 90.00 90.00 90.00 P 43 21 2 8 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 0.012028 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003241 0.00000