HEADER OXIDOREDUCTASE 14-DEC-17 5YZI TITLE CRYSTAL STRUCTURE OF MOUSE CYTOSOLIC ISOCITRATE DEHYDROGENASE TITLE 2 COMPLEXED WITH CADMIUM 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: IDH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS IDH, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.J.CHO,B.S.KANG REVDAT 3 27-MAR-24 5YZI 1 REMARK REVDAT 2 20-MAR-19 5YZI 1 JRNL REVDAT 1 04-JUL-18 5YZI 0 SPRSDE 04-JUL-18 5YZI 2CMV JRNL AUTH H.J.CHO,H.Y.CHO,J.W.PARK,O.S.KWON,H.S.LEE,T.L.HUH,B.S.KANG JRNL TITL NADP+-DEPENDENT CYTOSOLIC ISOCITRATE DEHYDROGENASE PROVIDES JRNL TITL 2 NADPH IN THE PRESENCE OF CADMIUM DUE TO THE MODERATE JRNL TITL 3 CHELATING EFFECT OF GLUTATHIONE. JRNL REF J. BIOL. INORG. CHEM. V. 23 849 2018 JRNL REFN ESSN 1432-1327 JRNL PMID 29923039 JRNL DOI 10.1007/S00775-018-1581-5 REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 29243 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1476 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 28.8676 - 5.5897 0.99 2636 145 0.1720 0.1894 REMARK 3 2 5.5897 - 4.4419 1.00 2602 143 0.1595 0.2179 REMARK 3 3 4.4419 - 3.8820 0.99 2588 150 0.1614 0.1840 REMARK 3 4 3.8820 - 3.5277 0.99 2567 141 0.1745 0.2462 REMARK 3 5 3.5277 - 3.2752 1.00 2593 151 0.1993 0.2534 REMARK 3 6 3.2752 - 3.0824 0.99 2560 143 0.2175 0.2623 REMARK 3 7 3.0824 - 2.9281 0.98 2553 133 0.2203 0.2952 REMARK 3 8 2.9281 - 2.8008 0.97 2486 129 0.2363 0.2656 REMARK 3 9 2.8008 - 2.6931 0.95 2480 115 0.2362 0.2816 REMARK 3 10 2.6931 - 2.6002 0.94 2478 112 0.2354 0.2992 REMARK 3 11 2.6002 - 2.5189 0.86 2224 114 0.2343 0.2664 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 6646 REMARK 3 ANGLE : 0.749 8990 REMARK 3 CHIRALITY : 0.047 977 REMARK 3 PLANARITY : 0.004 1143 REMARK 3 DIHEDRAL : 6.441 3964 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.3923 6.4123 33.2602 REMARK 3 T TENSOR REMARK 3 T11: 0.2340 T22: 0.2357 REMARK 3 T33: 0.3014 T12: 0.0462 REMARK 3 T13: -0.0069 T23: 0.0377 REMARK 3 L TENSOR REMARK 3 L11: 2.1998 L22: 1.9103 REMARK 3 L33: 3.6017 L12: 0.3332 REMARK 3 L13: -0.4963 L23: 0.7841 REMARK 3 S TENSOR REMARK 3 S11: 0.0108 S12: -0.1534 S13: 0.2235 REMARK 3 S21: -0.0078 S22: -0.0074 S23: 0.2873 REMARK 3 S31: -0.1694 S32: -0.4151 S33: -0.0012 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 134 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): 9.3670 -4.4348 36.8547 REMARK 3 T TENSOR REMARK 3 T11: 0.3957 T22: 0.3867 REMARK 3 T33: 0.3662 T12: 0.1559 REMARK 3 T13: -0.0303 T23: 0.0814 REMARK 3 L TENSOR REMARK 3 L11: 1.9752 L22: 0.8017 REMARK 3 L33: 2.8266 L12: -0.0040 REMARK 3 L13: 0.1250 L23: 0.2365 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: -0.3870 S13: -0.4026 REMARK 3 S21: 0.2980 S22: 0.0492 S23: -0.1637 REMARK 3 S31: 0.5488 S32: 0.4831 S33: -0.0370 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 286 THROUGH 412 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9976 -1.2060 23.8210 REMARK 3 T TENSOR REMARK 3 T11: 0.2232 T22: 0.4249 REMARK 3 T33: 0.3953 T12: -0.0446 REMARK 3 T13: -0.0074 T23: 0.0286 REMARK 3 L TENSOR REMARK 3 L11: 1.8918 L22: 1.5198 REMARK 3 L33: 4.1223 L12: 0.0577 REMARK 3 L13: -0.6740 L23: 0.9777 REMARK 3 S TENSOR REMARK 3 S11: -0.1473 S12: 0.2361 S13: 0.1468 REMARK 3 S21: -0.1447 S22: -0.0382 S23: 0.3328 REMARK 3 S31: 0.2665 S32: -0.9129 S33: 0.1523 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 4 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.0222 -7.9756 17.4781 REMARK 3 T TENSOR REMARK 3 T11: 0.4585 T22: 1.2100 REMARK 3 T33: 0.4738 T12: 0.3727 REMARK 3 T13: 0.0021 T23: -0.0014 REMARK 3 L TENSOR REMARK 3 L11: 1.3248 L22: 1.1756 REMARK 3 L33: 1.1801 L12: -0.5107 REMARK 3 L13: -0.7540 L23: 0.3135 REMARK 3 S TENSOR REMARK 3 S11: -0.0847 S12: -0.1830 S13: -0.2202 REMARK 3 S21: 0.1074 S22: 0.1707 S23: -0.3365 REMARK 3 S31: 0.5529 S32: 1.4646 S33: -0.0891 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 134 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): 12.4603 9.9974 23.9560 REMARK 3 T TENSOR REMARK 3 T11: 0.2441 T22: 0.3220 REMARK 3 T33: 0.3544 T12: -0.0357 REMARK 3 T13: 0.0024 T23: 0.0233 REMARK 3 L TENSOR REMARK 3 L11: 1.3127 L22: 0.6892 REMARK 3 L33: 5.2353 L12: 0.0575 REMARK 3 L13: 0.5233 L23: 0.5431 REMARK 3 S TENSOR REMARK 3 S11: -0.0532 S12: 0.0143 S13: 0.1009 REMARK 3 S21: -0.0414 S22: 0.0861 S23: -0.1574 REMARK 3 S31: -0.4621 S32: 0.8431 S33: -0.0457 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 286 THROUGH 411 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.3056 -14.6087 7.3238 REMARK 3 T TENSOR REMARK 3 T11: 0.5664 T22: 0.7820 REMARK 3 T33: 0.4551 T12: 0.3493 REMARK 3 T13: 0.0322 T23: -0.0533 REMARK 3 L TENSOR REMARK 3 L11: 3.1842 L22: 1.9201 REMARK 3 L33: 2.5883 L12: 0.2839 REMARK 3 L13: -0.2602 L23: -0.0564 REMARK 3 S TENSOR REMARK 3 S11: -0.1407 S12: 0.0199 S13: -0.4763 REMARK 3 S21: -0.2318 S22: 0.0304 S23: -0.1457 REMARK 3 S31: 0.7222 S32: 1.0049 S33: 0.0876 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 5YZI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-05 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 : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29260 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 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) : 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: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH 5.5 ,16% PEG REMARK 280 4000 , 20% ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.12300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.71400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.12300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 45.71400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 10460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 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 ARG A 3 REMARK 465 LYS A 413 REMARK 465 LEU A 414 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ARG B 3 REMARK 465 ALA B 412 REMARK 465 LYS B 413 REMARK 465 LEU B 414 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 87 CG CD CE NZ REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 LYS A 243 CG CD CE NZ REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 ASN B 53 CG OD1 ND2 REMARK 470 LYS B 58 CD CE NZ REMARK 470 LYS B 65 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU B 80 CG CD OE1 OE2 REMARK 470 LYS B 81 CG CD CE NZ REMARK 470 GLU B 84 CG CD OE1 OE2 REMARK 470 LYS B 233 CG CD CE NZ REMARK 470 LYS B 301 CD CE NZ REMARK 470 ARG B 314 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 321 CG CD CE NZ 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 -131.78 48.06 REMARK 500 ASN A 68 -7.68 71.69 REMARK 500 ASP A 79 -163.61 -103.05 REMARK 500 ASP A 137 -135.91 57.14 REMARK 500 ARG A 140 40.13 -142.49 REMARK 500 ASP A 160 -158.84 -82.20 REMARK 500 LYS A 212 53.82 -118.36 REMARK 500 MET A 290 66.51 -115.74 REMARK 500 GLU B 17 -134.77 50.95 REMARK 500 ILE B 31 -73.20 -111.34 REMARK 500 ASN B 68 -4.97 72.58 REMARK 500 ASP B 137 -137.33 58.05 REMARK 500 THR B 162 -166.78 -73.10 REMARK 500 LYS B 234 -31.05 -131.02 REMARK 500 MET B 290 67.31 -113.14 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 CD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP B 503 DBREF 5YZI A 1 414 UNP O88844 IDHC_MOUSE 1 414 DBREF 5YZI B 1 414 UNP O88844 IDHC_MOUSE 1 414 SEQRES 1 A 414 MET SER ARG LYS ILE GLN 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 LEU 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 TYR 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 THR GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 A 414 GLY ARG 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 LYS ASP GLY THR GLN LYS VAL THR TYR MET VAL SEQRES 14 A 414 HIS ASP 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 LYS SEQRES 19 A 414 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE CYS 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 ILE 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 SER ARG SEQRES 27 A 414 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN THR GLU SEQRES 28 A 414 LEU SER PHE PHE ALA LYS ALA LEU GLU ASP VAL CYS 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 ALA LYS LEU ALA GLN ALA LYS LEU SEQRES 1 B 414 MET SER ARG LYS ILE GLN 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 LEU 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 TYR 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 THR GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 B 414 GLY ARG 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 LYS ASP GLY THR GLN LYS VAL THR TYR MET VAL SEQRES 14 B 414 HIS ASP 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 LYS SEQRES 19 B 414 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE CYS 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 ILE 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 SER ARG SEQRES 27 B 414 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN THR GLU SEQRES 28 B 414 LEU SER PHE PHE ALA LYS ALA LEU GLU ASP VAL CYS 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 ALA LYS LEU ALA GLN ALA LYS LEU HET CD A 501 1 HET NAP A 502 48 HET CD B 501 1 HET CD B 502 1 HET NAP B 503 48 HETNAM CD CADMIUM ION HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 CD 3(CD 2+) FORMUL 4 NAP 2(C21 H28 N7 O17 P3) FORMUL 8 HOH *129(H2 O) HELIX 1 AA1 ASP A 16 LEU A 30 1 15 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 GLY A 136 ALA A 141 5 6 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 GLN A 242 1 8 HELIX 10 AB1 ILE A 251 SER A 261 1 11 HELIX 11 AB2 LYS A 270 GLY A 286 1 17 HELIX 12 AB3 VAL A 312 LYS A 321 1 10 HELIX 13 AB4 PRO A 329 ASN A 348 1 20 HELIX 14 AB5 ASN A 349 ALA A 369 1 21 HELIX 15 AB6 THR A 373 GLY A 382 1 10 HELIX 16 AB7 LEU A 383 VAL A 386 5 4 HELIX 17 AB8 GLN A 387 TYR A 391 5 5 HELIX 18 AB9 ASN A 393 ALA A 412 1 20 HELIX 19 AC1 ASP B 16 LEU B 30 1 15 HELIX 20 AC2 GLY B 45 THR B 52 1 8 HELIX 21 AC3 ASP B 54 ASN B 68 1 15 HELIX 22 AC4 ASP B 79 LYS B 87 1 9 HELIX 23 AC5 SER B 94 GLY B 104 1 11 HELIX 24 AC6 GLY B 136 ALA B 141 5 6 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 SER B 261 1 11 HELIX 29 AD2 LYS B 270 GLY B 286 1 17 HELIX 30 AD3 VAL B 312 LYS B 321 1 10 HELIX 31 AD4 PRO B 329 ASN B 348 1 20 HELIX 32 AD5 ASN B 349 ALA B 369 1 21 HELIX 33 AD6 THR B 373 GLY B 382 1 10 HELIX 34 AD7 LEU B 383 VAL B 386 5 4 HELIX 35 AD8 GLN B 387 TYR B 391 5 5 HELIX 36 AD9 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 71 N VAL A 11 SHEET 4 AA110 VAL A 303 ALA A 307 1 O ALA A 305 N GLY A 70 SHEET 5 AA110 MET A 291 ILE A 296 -1 N LEU A 295 O GLU A 304 SHEET 6 AA110 THR A 106 ALA A 111 -1 N GLU A 110 O THR A 292 SHEET 7 AA110 ILE A 128 HIS A 133 -1 O ARG A 132 N VAL A 107 SHEET 8 AA110 PHE A 265 CYS A 269 1 O CYS A 269 N GLY A 131 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 THR A 142 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 GLY A 150 O PHE A 172 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 PHE B 172 N GLY B 150 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 GLU B 306 1 O ALA B 305 N GLY B 70 SHEET 5 AA410 MET B 291 ILE B 296 -1 N LEU B 295 O GLU B 304 SHEET 6 AA410 THR B 106 ALA B 111 -1 N GLU B 110 O THR B 292 SHEET 7 AA410 ILE B 128 HIS B 133 -1 O ARG B 132 N VAL B 107 SHEET 8 AA410 PHE B 265 CYS B 269 1 O TRP B 267 N GLY B 131 SHEET 9 AA410 LEU B 207 THR B 211 1 N TYR B 208 O ALA B 268 SHEET 10 AA410 TYR B 246 LEU B 250 1 O ARG B 249 N LEU B 209 LINK SG CYS B 245 CD CD B 502 1555 1555 3.04 SITE 1 AC1 3 ASP A 275 ASP A 279 ASP B 252 SITE 1 AC2 26 LYS A 72 THR A 75 THR A 77 ARG A 82 SITE 2 AC2 26 ASN A 96 ALA A 307 HIS A 309 GLY A 310 SITE 3 AC2 26 THR A 311 VAL A 312 THR A 313 ARG A 314 SITE 4 AC2 26 HIS A 315 THR A 327 ASN A 328 HOH A 603 SITE 5 AC2 26 HOH A 605 HOH A 611 HOH A 612 HOH A 636 SITE 6 AC2 26 HOH A 643 HOH A 656 ASP B 253 GLN B 257 SITE 7 AC2 26 LYS B 260 HOH B 626 SITE 1 AC3 4 ASP A 252 ASP B 275 ASP B 279 ALA B 308 SITE 1 AC4 3 CYS B 245 GLU B 247 HOH B 638 SITE 1 AC5 19 ASP A 253 LYS A 260 LYS B 72 ALA B 74 SITE 2 AC5 19 THR B 75 ILE B 76 THR B 77 ASN B 96 SITE 3 AC5 19 LEU B 288 GLU B 306 ALA B 307 HIS B 309 SITE 4 AC5 19 GLY B 310 THR B 311 VAL B 312 THR B 313 SITE 5 AC5 19 ARG B 314 HIS B 315 ASN B 328 CRYST1 98.246 91.428 109.724 90.00 113.65 90.00 C 1 2 1 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 0.010179 0.000000 0.004457 0.00000 SCALE2 0.000000 0.010938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009949 0.00000