HEADER OXIDOREDUCTASE 10-JUL-25 9VT7 TITLE THE CRYSTAL STRUCTURE OF IDH1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDH,IDH1,CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE,IDPC, COMPND 5 NADP(+)-SPECIFIC ICDH,OXALOSUCCINATE DECARBOXYLASE; COMPND 6 EC: 1.1.1.42; COMPND 7 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 KEYWDS COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.H.WANG,Q.J.XIAO,W.M.QIN REVDAT 1 15-JUL-26 9VT7 0 JRNL AUTH W.H.WANG,Q.J.XIAO,W.M.QIN JRNL TITL THE CRYSTAL STRUCTURE OF IDH1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19_4092: ???) 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) : 2.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 63958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 3192 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 49.8700 - 5.9100 0.99 2708 138 0.1563 0.1732 REMARK 3 2 5.9100 - 4.6900 1.00 2676 146 0.1506 0.1627 REMARK 3 3 4.6900 - 4.1000 1.00 2644 151 0.1356 0.1666 REMARK 3 4 4.1000 - 3.7300 1.00 2657 133 0.1531 0.1710 REMARK 3 5 3.7300 - 3.4600 0.99 2621 121 0.1741 0.2031 REMARK 3 6 3.4600 - 3.2500 0.99 2646 162 0.1874 0.2343 REMARK 3 7 3.2500 - 3.0900 1.00 2614 152 0.2013 0.2343 REMARK 3 8 3.0900 - 2.9600 1.00 2631 133 0.1978 0.2080 REMARK 3 9 2.9600 - 2.8400 1.00 2651 141 0.1985 0.2604 REMARK 3 10 2.8400 - 2.7500 1.00 2649 148 0.1930 0.2570 REMARK 3 11 2.7500 - 2.6600 1.00 2636 143 0.1932 0.2369 REMARK 3 12 2.6600 - 2.5800 1.00 2646 146 0.1989 0.2516 REMARK 3 13 2.5800 - 2.5200 1.00 2620 131 0.2033 0.2473 REMARK 3 14 2.5200 - 2.4500 1.00 2663 131 0.2130 0.2399 REMARK 3 15 2.4500 - 2.4000 1.00 2656 151 0.2007 0.2362 REMARK 3 16 2.4000 - 2.3500 1.00 2636 141 0.2143 0.2478 REMARK 3 17 2.3500 - 2.3000 1.00 2609 128 0.2103 0.2550 REMARK 3 18 2.3000 - 2.2600 1.00 2677 133 0.2067 0.2364 REMARK 3 19 2.2600 - 2.2200 1.00 2619 124 0.2139 0.2527 REMARK 3 20 2.2200 - 2.1800 1.00 2621 127 0.2207 0.2821 REMARK 3 21 2.1800 - 2.1400 0.99 2689 133 0.2273 0.2687 REMARK 3 22 2.1400 - 2.1100 1.00 2585 127 0.2408 0.2655 REMARK 3 23 2.1100 - 2.0800 0.99 2612 152 0.2565 0.3061 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.400 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 : 0.008 6732 REMARK 3 ANGLE : 0.889 9088 REMARK 3 CHIRALITY : 0.052 981 REMARK 3 PLANARITY : 0.007 1162 REMARK 3 DIHEDRAL : 7.591 899 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 3 THROUGH 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.3576 41.2339 32.9861 REMARK 3 T TENSOR REMARK 3 T11: 0.1989 T22: 0.2323 REMARK 3 T33: 0.1977 T12: -0.0213 REMARK 3 T13: -0.0075 T23: -0.0408 REMARK 3 L TENSOR REMARK 3 L11: 0.5402 L22: 0.4566 REMARK 3 L33: 0.7956 L12: 0.1682 REMARK 3 L13: -0.5291 L23: -0.1747 REMARK 3 S TENSOR REMARK 3 S11: 0.0643 S12: -0.1720 S13: 0.0925 REMARK 3 S21: 0.0192 S22: 0.0065 S23: 0.0280 REMARK 3 S31: -0.0012 S32: 0.1350 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.1984 19.5663 40.4513 REMARK 3 T TENSOR REMARK 3 T11: 0.2636 T22: 0.1687 REMARK 3 T33: 0.2262 T12: -0.0111 REMARK 3 T13: 0.0511 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 0.1663 L22: 0.8174 REMARK 3 L33: 1.1196 L12: -0.0609 REMARK 3 L13: -0.2170 L23: 0.0829 REMARK 3 S TENSOR REMARK 3 S11: 0.0947 S12: -0.0045 S13: 0.0002 REMARK 3 S21: 0.0155 S22: 0.0697 S23: 0.0805 REMARK 3 S31: -0.3401 S32: -0.0209 S33: 0.0012 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 286 THROUGH 415 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0016 42.0926 19.3827 REMARK 3 T TENSOR REMARK 3 T11: 0.1804 T22: 0.1696 REMARK 3 T33: 0.2006 T12: -0.0134 REMARK 3 T13: -0.0106 T23: 0.0259 REMARK 3 L TENSOR REMARK 3 L11: 0.3430 L22: 0.4641 REMARK 3 L33: 0.7747 L12: 0.0208 REMARK 3 L13: -0.4043 L23: -0.0142 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: 0.0104 S13: 0.0307 REMARK 3 S21: -0.0338 S22: 0.0711 S23: 0.0817 REMARK 3 S31: -0.0291 S32: -0.0051 S33: 0.0003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 3 THROUGH 43 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.8383 -15.3483 21.2338 REMARK 3 T TENSOR REMARK 3 T11: 0.2401 T22: 0.1877 REMARK 3 T33: 0.1858 T12: -0.0351 REMARK 3 T13: -0.0218 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.2472 L22: 0.1038 REMARK 3 L33: 0.1207 L12: 0.2143 REMARK 3 L13: 0.0174 L23: 0.0496 REMARK 3 S TENSOR REMARK 3 S11: -0.0061 S12: -0.0911 S13: -0.0922 REMARK 3 S21: 0.0616 S22: -0.0956 S23: 0.0290 REMARK 3 S31: 0.3924 S32: -0.2412 S33: -0.0004 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 44 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.3025 -6.4463 37.1801 REMARK 3 T TENSOR REMARK 3 T11: 0.2117 T22: 0.3617 REMARK 3 T33: 0.2112 T12: -0.0492 REMARK 3 T13: -0.0105 T23: -0.0367 REMARK 3 L TENSOR REMARK 3 L11: 0.1766 L22: 0.0770 REMARK 3 L33: 0.2786 L12: 0.0643 REMARK 3 L13: 0.1097 L23: 0.1255 REMARK 3 S TENSOR REMARK 3 S11: 0.1004 S12: -0.3774 S13: 0.0008 REMARK 3 S21: 0.0205 S22: -0.0700 S23: 0.0230 REMARK 3 S31: 0.1189 S32: -0.1406 S33: 0.0001 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 95 THROUGH 133 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.8022 3.8281 22.3501 REMARK 3 T TENSOR REMARK 3 T11: 0.1958 T22: 0.1897 REMARK 3 T33: 0.2077 T12: -0.0336 REMARK 3 T13: 0.0103 T23: -0.0177 REMARK 3 L TENSOR REMARK 3 L11: 0.0092 L22: 0.1727 REMARK 3 L33: 0.0821 L12: 0.0468 REMARK 3 L13: 0.0129 L23: 0.1531 REMARK 3 S TENSOR REMARK 3 S11: 0.0645 S12: -0.0697 S13: 0.0595 REMARK 3 S21: -0.0834 S22: 0.0855 S23: -0.0416 REMARK 3 S31: -0.1152 S32: 0.0485 S33: -0.0001 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 134 THROUGH 285 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.0105 8.9608 36.8423 REMARK 3 T TENSOR REMARK 3 T11: 0.1539 T22: 0.2468 REMARK 3 T33: 0.2315 T12: -0.0562 REMARK 3 T13: 0.0195 T23: -0.0521 REMARK 3 L TENSOR REMARK 3 L11: 0.2979 L22: 0.4602 REMARK 3 L33: 0.7749 L12: -0.0107 REMARK 3 L13: 0.1134 L23: 0.0663 REMARK 3 S TENSOR REMARK 3 S11: 0.0700 S12: 0.0070 S13: -0.0486 REMARK 3 S21: 0.0035 S22: 0.0933 S23: -0.0908 REMARK 3 S31: -0.1628 S32: 0.3002 S33: 0.0101 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 286 THROUGH 349 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.6724 -5.2094 21.6207 REMARK 3 T TENSOR REMARK 3 T11: 0.1704 T22: 0.1598 REMARK 3 T33: 0.1938 T12: -0.0065 REMARK 3 T13: -0.0272 T23: -0.0186 REMARK 3 L TENSOR REMARK 3 L11: 0.1743 L22: 0.4152 REMARK 3 L33: 0.4679 L12: 0.1197 REMARK 3 L13: -0.0695 L23: 0.1890 REMARK 3 S TENSOR REMARK 3 S11: 0.0991 S12: -0.0556 S13: 0.0787 REMARK 3 S21: -0.0410 S22: -0.0272 S23: -0.0311 REMARK 3 S31: 0.0330 S32: 0.0449 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 350 THROUGH 416 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.6686 -4.3118 6.7310 REMARK 3 T TENSOR REMARK 3 T11: 0.2401 T22: 0.1734 REMARK 3 T33: 0.1719 T12: 0.0056 REMARK 3 T13: -0.0129 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.1728 L22: 0.0940 REMARK 3 L33: 0.1948 L12: -0.2742 REMARK 3 L13: -0.1329 L23: 0.2875 REMARK 3 S TENSOR REMARK 3 S11: 0.0547 S12: 0.0992 S13: 0.0299 REMARK 3 S21: -0.1719 S22: -0.0207 S23: -0.0556 REMARK 3 S31: -0.0125 S32: 0.0296 S33: -0.0000 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 9VT7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 16-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1300061378. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-24 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64133 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.080 REMARK 200 RESOLUTION RANGE LOW (A) : 57.370 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.88900 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 (%): 57.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LI SULFATE,O.1 M HEPES (PH 7.4), REMARK 280 20% PEG 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 50.07950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.27600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.07950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 54.27600 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: 7170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 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 LEU A 416 REMARK 465 GLU A 417 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 GLU B 417 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 -131.95 53.91 REMARK 500 ILE A 31 -63.80 -99.95 REMARK 500 ASN A 68 -12.80 73.07 REMARK 500 ASP A 79 -166.47 -124.12 REMARK 500 ALA A 134 36.22 -89.78 REMARK 500 ASP A 137 -136.48 57.39 REMARK 500 HIS A 170 143.50 -171.73 REMARK 500 LEU A 216 76.52 -101.74 REMARK 500 LYS A 243 45.89 32.68 REMARK 500 GLU B 17 -136.06 57.72 REMARK 500 ILE B 31 -63.13 -102.85 REMARK 500 ASN B 68 -5.68 77.28 REMARK 500 ASP B 79 -165.61 -105.90 REMARK 500 ASP B 137 -130.42 54.94 REMARK 500 GLN B 234 -30.66 -136.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 792 DISTANCE = 6.01 ANGSTROMS DBREF 9VT7 A 1 414 UNP O75874 IDHC_HUMAN 1 414 DBREF 9VT7 B 1 414 UNP O75874 IDHC_HUMAN 1 414 SEQADV 9VT7 SER A 415 UNP O75874 EXPRESSION TAG SEQADV 9VT7 LEU A 416 UNP O75874 EXPRESSION TAG SEQADV 9VT7 GLU A 417 UNP O75874 EXPRESSION TAG SEQADV 9VT7 SER B 415 UNP O75874 EXPRESSION TAG SEQADV 9VT7 LEU B 416 UNP O75874 EXPRESSION TAG SEQADV 9VT7 GLU B 417 UNP O75874 EXPRESSION TAG SEQRES 1 A 417 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 A 417 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 A 417 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 A 417 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 A 417 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 A 417 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 417 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 A 417 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 A 417 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 A 417 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 A 417 GLY ARG HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 A 417 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 A 417 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 A 417 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 A 417 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 A 417 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 A 417 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 A 417 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 A 417 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 A 417 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 A 417 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 A 417 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 A 417 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 A 417 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 A 417 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 A 417 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 A 417 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 A 417 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 A 417 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 A 417 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 A 417 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 A 417 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU SER LEU SEQRES 33 A 417 GLU SEQRES 1 B 417 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 B 417 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 B 417 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 B 417 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 B 417 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 B 417 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 B 417 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 B 417 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 B 417 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 B 417 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 B 417 GLY ARG HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 B 417 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 B 417 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 B 417 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 B 417 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 B 417 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 B 417 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 B 417 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 B 417 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 B 417 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 B 417 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 B 417 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 B 417 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 B 417 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 B 417 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 B 417 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 B 417 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 B 417 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 B 417 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 B 417 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 B 417 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 B 417 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU SER LEU SEQRES 33 B 417 GLU HET NAP A 501 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 HOH *563(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 SER A 287 GLY A 289 5 3 HELIX 13 AB4 VAL A 312 GLN A 320 1 9 HELIX 14 AB5 PRO A 329 ASN A 348 1 20 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 SER A 415 1 23 HELIX 20 AC2 ASP B 16 ILE B 31 1 16 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 GLY B 136 ALA B 141 5 6 HELIX 26 AC8 ASP B 186 GLY B 204 1 19 HELIX 27 AC9 LYS B 218 TYR B 235 1 18 HELIX 28 AD1 TYR B 235 GLN B 242 1 8 HELIX 29 AD2 ILE B 251 SER B 261 1 11 HELIX 30 AD3 LYS B 270 TYR B 285 1 16 HELIX 31 AD4 VAL B 312 GLN B 320 1 9 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 LEU B 416 1 24 SHEET 1 AA110 VAL A 35 ASP A 43 0 SHEET 2 AA110 ILE A 5 GLN A 14 1 N GLU A 12 O TYR A 42 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 ARG A 132 -1 O ILE A 130 N ARG A 109 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 THR B 142 O GLY B 181 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 THR B 155 N GLU A 153 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 GLY B 7 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 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 THR B 106 O VAL B 296 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 CRYST1 100.159 108.552 100.393 90.00 95.26 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 0.009984 0.000000 0.000919 0.00000 SCALE2 0.000000 0.009212 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010003 0.00000 CONECT 6555 6556 6557 6558 6577 CONECT 6556 6555 CONECT 6557 6555 CONECT 6558 6555 6559 CONECT 6559 6558 6560 CONECT 6560 6559 6561 6562 CONECT 6561 6560 6566 CONECT 6562 6560 6563 6564 CONECT 6563 6562 CONECT 6564 6562 6565 6566 CONECT 6565 6564 6599 CONECT 6566 6561 6564 6567 CONECT 6567 6566 6568 6576 CONECT 6568 6567 6569 CONECT 6569 6568 6570 CONECT 6570 6569 6571 6576 CONECT 6571 6570 6572 6573 CONECT 6572 6571 CONECT 6573 6571 6574 CONECT 6574 6573 6575 CONECT 6575 6574 6576 CONECT 6576 6567 6570 6575 CONECT 6577 6555 6578 CONECT 6578 6577 6579 6580 6581 CONECT 6579 6578 CONECT 6580 6578 CONECT 6581 6578 6582 CONECT 6582 6581 6583 CONECT 6583 6582 6584 6585 CONECT 6584 6583 6589 CONECT 6585 6583 6586 6587 CONECT 6586 6585 CONECT 6587 6585 6588 6589 CONECT 6588 6587 CONECT 6589 6584 6587 6590 CONECT 6590 6589 6591 6598 CONECT 6591 6590 6592 CONECT 6592 6591 6593 6596 CONECT 6593 6592 6594 6595 CONECT 6594 6593 CONECT 6595 6593 CONECT 6596 6592 6597 CONECT 6597 6596 6598 CONECT 6598 6590 6597 CONECT 6599 6565 6600 6601 6602 CONECT 6600 6599 CONECT 6601 6599 CONECT 6602 6599 MASTER 408 0 1 37 28 0 0 6 7163 2 48 66 END