HEADER OXIDOREDUCTASE 21-SEP-17 5YFN TITLE HUMAN ISOCITRATE DEHYDROGENASE 1 BOUND WITH ISOCITRATE 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: 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 IDH1, ISOCITRATE, NADPH REGENERATION, CYTOSOLIC PROTEIN, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.NORDLUND,D.CHEN,A.JANSSON,A.LARSSON REVDAT 2 22-NOV-23 5YFN 1 LINK REVDAT 1 25-OCT-17 5YFN 0 JRNL AUTH P.NORDLUND,D.CHEN,A.JANSSON,A.LARSSON JRNL TITL HUMAN ISOCITRATE DEHYDROGENASE 1 BOUND WITH ISOCITRATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 43212 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2300 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3151 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 165 REMARK 3 BIN FREE R VALUE : 0.3290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6489 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 205 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.28000 REMARK 3 B22 (A**2) : 1.58000 REMARK 3 B33 (A**2) : -3.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.99000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.284 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.227 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.343 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6659 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6105 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8986 ; 1.847 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14205 ; 1.082 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 821 ; 7.563 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 307 ;38.171 ;24.951 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1183 ;18.247 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;20.732 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 973 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7412 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1339 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5YFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300005199. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-12 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95400 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45512 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 41.798 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 12.7000 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) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : 0.32500 REMARK 200 FOR SHELL : 2.300 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: 1T09 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES SODIUM PH7.5, 0.8 M SODIUM REMARK 280 PHOSPHATE, 0.8 M POTASSIUM PHOSPHATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 32.10614 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.25594 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.10614 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 65.25594 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: 8580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 33350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 ALA A 412 REMARK 465 LYS A 413 REMARK 465 LEU A 414 REMARK 465 ARG B 314 REMARK 465 HIS B 315 REMARK 465 TYR B 316 REMARK 465 ARG B 317 REMARK 465 MET B 318 REMARK 465 TYR B 319 REMARK 465 GLN B 320 REMARK 465 LYS B 321 REMARK 465 GLY B 322 REMARK 465 GLN B 323 REMARK 465 GLU B 324 REMARK 465 THR B 325 REMARK 465 SER B 326 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 LEU A -5 CG CD1 CD2 REMARK 470 GLN A -2 CG CD OE1 NE2 REMARK 470 MET A 0 CG SD CE REMARK 470 LYS A 3 CG CD CE NZ REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 GLU A 174 CG CD OE1 OE2 REMARK 470 ARG A 314 CG CD NE CZ NH1 NH2 REMARK 470 MET B 0 CG SD CE REMARK 470 LYS B 3 CG CD CE NZ REMARK 470 LYS B 350 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS B 269 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 ASP B 273 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 CYS B 379 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 17 -130.36 38.50 REMARK 500 ILE A 31 -68.04 -99.76 REMARK 500 ASN A 68 -12.71 80.36 REMARK 500 LYS A 87 72.98 29.90 REMARK 500 ASP A 137 -139.13 46.67 REMARK 500 ARG A 140 36.74 -155.91 REMARK 500 THR A 162 -71.21 -47.95 REMARK 500 GLN A 163 128.58 -176.08 REMARK 500 ASN A 271 -52.20 -27.31 REMARK 500 SER A 287 119.10 -162.52 REMARK 500 THR A 311 -36.58 82.65 REMARK 500 VAL A 312 71.48 33.76 REMARK 500 GLU B 17 -140.36 60.20 REMARK 500 ILE B 31 -69.53 -97.89 REMARK 500 ASN B 53 43.00 36.89 REMARK 500 ASN B 68 -6.78 76.48 REMARK 500 ASP B 137 -132.75 54.82 REMARK 500 ASP B 160 -139.66 -76.78 REMARK 500 ASN B 271 -66.37 -27.40 REMARK 500 ASP B 299 6.22 -64.97 REMARK 500 LYS B 301 -55.87 -158.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 252 OD2 REMARK 620 2 ICT A 505 O1 150.2 REMARK 620 3 ICT A 505 O7 75.5 74.9 REMARK 620 4 ASP B 275 OD1 89.0 93.9 88.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 275 OD1 REMARK 620 2 ICT A 502 O2 93.9 REMARK 620 3 ICT A 502 O7 77.4 65.8 REMARK 620 4 ASP B 252 OD2 78.4 137.0 71.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ICT A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ICT A 505 DBREF 5YFN A 1 414 UNP O75874 IDHC_HUMAN 1 414 DBREF 5YFN B 1 414 UNP O75874 IDHC_HUMAN 1 414 SEQADV 5YFN ASN A -6 UNP O75874 EXPRESSION TAG SEQADV 5YFN LEU A -5 UNP O75874 EXPRESSION TAG SEQADV 5YFN TYR A -4 UNP O75874 EXPRESSION TAG SEQADV 5YFN PHE A -3 UNP O75874 EXPRESSION TAG SEQADV 5YFN GLN A -2 UNP O75874 EXPRESSION TAG SEQADV 5YFN SER A -1 UNP O75874 EXPRESSION TAG SEQADV 5YFN MET A 0 UNP O75874 EXPRESSION TAG SEQADV 5YFN ASN B -6 UNP O75874 EXPRESSION TAG SEQADV 5YFN LEU B -5 UNP O75874 EXPRESSION TAG SEQADV 5YFN TYR B -4 UNP O75874 EXPRESSION TAG SEQADV 5YFN PHE B -3 UNP O75874 EXPRESSION TAG SEQADV 5YFN GLN B -2 UNP O75874 EXPRESSION TAG SEQADV 5YFN SER B -1 UNP O75874 EXPRESSION TAG SEQADV 5YFN MET B 0 UNP O75874 EXPRESSION TAG SEQRES 1 A 421 ASN LEU TYR PHE GLN SER MET MET SER LYS LYS ILE SER SEQRES 2 A 421 GLY GLY SER VAL VAL GLU MET GLN GLY ASP GLU MET THR SEQRES 3 A 421 ARG ILE ILE TRP GLU LEU ILE LYS GLU LYS LEU ILE PHE SEQRES 4 A 421 PRO TYR VAL GLU LEU ASP LEU HIS SER TYR ASP LEU GLY SEQRES 5 A 421 ILE GLU ASN ARG ASP ALA THR ASN ASP GLN VAL THR LYS SEQRES 6 A 421 ASP ALA ALA GLU ALA ILE LYS LYS HIS ASN VAL GLY VAL SEQRES 7 A 421 LYS CYS ALA THR ILE THR PRO ASP GLU LYS ARG VAL GLU SEQRES 8 A 421 GLU PHE LYS LEU LYS GLN MET TRP LYS SER PRO ASN GLY SEQRES 9 A 421 THR ILE ARG ASN ILE LEU GLY GLY THR VAL PHE ARG GLU SEQRES 10 A 421 ALA ILE ILE CYS LYS ASN ILE PRO ARG LEU VAL SER GLY SEQRES 11 A 421 TRP VAL LYS PRO ILE ILE ILE GLY ARG HIS ALA TYR GLY SEQRES 12 A 421 ASP GLN TYR ARG ALA THR ASP PHE VAL VAL PRO GLY PRO SEQRES 13 A 421 GLY LYS VAL GLU ILE THR TYR THR PRO SER ASP GLY THR SEQRES 14 A 421 GLN LYS VAL THR TYR LEU VAL HIS ASN PHE GLU GLU GLY SEQRES 15 A 421 GLY GLY VAL ALA MET GLY MET TYR ASN GLN ASP LYS SER SEQRES 16 A 421 ILE GLU ASP PHE ALA HIS SER SER PHE GLN MET ALA LEU SEQRES 17 A 421 SER LYS GLY TRP PRO LEU TYR LEU SER THR LYS ASN THR SEQRES 18 A 421 ILE LEU LYS LYS TYR ASP GLY ARG PHE LYS ASP ILE PHE SEQRES 19 A 421 GLN GLU ILE TYR ASP LYS GLN TYR LYS SER GLN PHE GLU SEQRES 20 A 421 ALA GLN LYS ILE TRP TYR GLU HIS ARG LEU ILE ASP ASP SEQRES 21 A 421 MET VAL ALA GLN ALA MET LYS SER GLU GLY GLY PHE ILE SEQRES 22 A 421 TRP ALA CYS LYS ASN TYR ASP GLY ASP VAL GLN SER ASP SEQRES 23 A 421 SER VAL ALA GLN GLY TYR GLY SER LEU GLY MET MET THR SEQRES 24 A 421 SER VAL LEU VAL CYS PRO ASP GLY LYS THR VAL GLU ALA SEQRES 25 A 421 GLU ALA ALA HIS GLY THR VAL THR ARG HIS TYR ARG MET SEQRES 26 A 421 TYR GLN LYS GLY GLN GLU THR SER THR ASN PRO ILE ALA SEQRES 27 A 421 SER ILE PHE ALA TRP THR ARG GLY LEU ALA HIS ARG ALA SEQRES 28 A 421 LYS LEU ASP ASN ASN LYS GLU LEU ALA PHE PHE ALA ASN SEQRES 29 A 421 ALA LEU GLU GLU VAL SER ILE GLU THR ILE GLU ALA GLY SEQRES 30 A 421 PHE MET THR LYS ASP LEU ALA ALA CYS ILE LYS GLY LEU SEQRES 31 A 421 PRO ASN VAL GLN ARG SER ASP TYR LEU ASN THR PHE GLU SEQRES 32 A 421 PHE MET ASP LYS LEU GLY GLU ASN LEU LYS ILE LYS LEU SEQRES 33 A 421 ALA GLN ALA LYS LEU SEQRES 1 B 421 ASN LEU TYR PHE GLN SER MET MET SER LYS LYS ILE SER SEQRES 2 B 421 GLY GLY SER VAL VAL GLU MET GLN GLY ASP GLU MET THR SEQRES 3 B 421 ARG ILE ILE TRP GLU LEU ILE LYS GLU LYS LEU ILE PHE SEQRES 4 B 421 PRO TYR VAL GLU LEU ASP LEU HIS SER TYR ASP LEU GLY SEQRES 5 B 421 ILE GLU ASN ARG ASP ALA THR ASN ASP GLN VAL THR LYS SEQRES 6 B 421 ASP ALA ALA GLU ALA ILE LYS LYS HIS ASN VAL GLY VAL SEQRES 7 B 421 LYS CYS ALA THR ILE THR PRO ASP GLU LYS ARG VAL GLU SEQRES 8 B 421 GLU PHE LYS LEU LYS GLN MET TRP LYS SER PRO ASN GLY SEQRES 9 B 421 THR ILE ARG ASN ILE LEU GLY GLY THR VAL PHE ARG GLU SEQRES 10 B 421 ALA ILE ILE CYS LYS ASN ILE PRO ARG LEU VAL SER GLY SEQRES 11 B 421 TRP VAL LYS PRO ILE ILE ILE GLY ARG HIS ALA TYR GLY SEQRES 12 B 421 ASP GLN TYR ARG ALA THR ASP PHE VAL VAL PRO GLY PRO SEQRES 13 B 421 GLY LYS VAL GLU ILE THR TYR THR PRO SER ASP GLY THR SEQRES 14 B 421 GLN LYS VAL THR TYR LEU VAL HIS ASN PHE GLU GLU GLY SEQRES 15 B 421 GLY GLY VAL ALA MET GLY MET TYR ASN GLN ASP LYS SER SEQRES 16 B 421 ILE GLU ASP PHE ALA HIS SER SER PHE GLN MET ALA LEU SEQRES 17 B 421 SER LYS GLY TRP PRO LEU TYR LEU SER THR LYS ASN THR SEQRES 18 B 421 ILE LEU LYS LYS TYR ASP GLY ARG PHE LYS ASP ILE PHE SEQRES 19 B 421 GLN GLU ILE TYR ASP LYS GLN TYR LYS SER GLN PHE GLU SEQRES 20 B 421 ALA GLN LYS ILE TRP TYR GLU HIS ARG LEU ILE ASP ASP SEQRES 21 B 421 MET VAL ALA GLN ALA MET LYS SER GLU GLY GLY PHE ILE SEQRES 22 B 421 TRP ALA CYS LYS ASN TYR ASP GLY ASP VAL GLN SER ASP SEQRES 23 B 421 SER VAL ALA GLN GLY TYR GLY SER LEU GLY MET MET THR SEQRES 24 B 421 SER VAL LEU VAL CYS PRO ASP GLY LYS THR VAL GLU ALA SEQRES 25 B 421 GLU ALA ALA HIS GLY THR VAL THR ARG HIS TYR ARG MET SEQRES 26 B 421 TYR GLN LYS GLY GLN GLU THR SER THR ASN PRO ILE ALA SEQRES 27 B 421 SER ILE PHE ALA TRP THR ARG GLY LEU ALA HIS ARG ALA SEQRES 28 B 421 LYS LEU ASP ASN ASN LYS GLU LEU ALA PHE PHE ALA ASN SEQRES 29 B 421 ALA LEU GLU GLU VAL SER ILE GLU THR ILE GLU ALA GLY SEQRES 30 B 421 PHE MET THR LYS ASP LEU ALA ALA CYS ILE LYS GLY LEU SEQRES 31 B 421 PRO ASN VAL GLN ARG SER ASP TYR LEU ASN THR PHE GLU SEQRES 32 B 421 PHE MET ASP LYS LEU GLY GLU ASN LEU LYS ILE LYS LEU SEQRES 33 B 421 ALA GLN ALA LYS LEU HET MG A 501 1 HET ICT A 502 18 HET MG A 503 1 HET K A 504 1 HET ICT A 505 18 HET K B 501 1 HETNAM MG MAGNESIUM ION HETNAM ICT ISOCITRIC ACID HETNAM K POTASSIUM ION FORMUL 3 MG 2(MG 2+) FORMUL 4 ICT 2(C6 H8 O7) FORMUL 6 K 2(K 1+) FORMUL 9 HOH *205(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 LYS A 260 1 10 HELIX 11 AB2 LYS A 270 TYR A 285 1 16 HELIX 12 AB3 VAL A 312 LYS A 321 1 10 HELIX 13 AB4 PRO A 329 ASP A 347 1 19 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 GLN A 411 1 19 HELIX 19 AC1 ASP B 16 ILE B 31 1 16 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 PHE B 86 1 8 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 TYR B 285 1 16 HELIX 30 AD3 PRO B 329 ASP B 347 1 19 HELIX 31 AD4 ASN B 349 ALA B 369 1 21 HELIX 32 AD5 THR B 373 GLY B 382 1 10 HELIX 33 AD6 LEU B 383 VAL B 386 5 4 HELIX 34 AD7 GLN B 387 TYR B 391 5 5 HELIX 35 AD8 ASN B 393 ALA B 412 1 20 SHEET 1 AA110 VAL A 35 ASP A 43 0 SHEET 2 AA110 ILE A 5 GLN A 14 1 N ILE A 5 O GLU A 36 SHEET 3 AA110 VAL A 69 LYS A 72 1 O VAL A 69 N VAL A 11 SHEET 4 AA110 VAL A 303 GLU A 306 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 THR A 106 O VAL A 296 SHEET 7 AA110 ILE A 128 HIS A 133 -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 MET B 182 N MET A 180 SHEET 4 AA2 4 THR B 142 VAL B 146 -1 N VAL B 146 O GLY B 177 SHEET 1 AA3 4 VAL A 165 PHE A 172 0 SHEET 2 AA3 4 GLY A 150 PRO A 158 -1 N ILE A 154 O TYR A 167 SHEET 3 AA3 4 GLY B 150 PRO B 158 -1 O 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 GLN B 14 O TYR B 42 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 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 CYS B 269 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 OD2 ASP A 252 MG MG A 503 1555 1555 2.23 LINK OD1 ASP A 275 MG MG A 501 1555 1555 2.21 LINK MG MG A 501 O2 ICT A 502 1555 1555 2.74 LINK MG MG A 501 O7 ICT A 502 1555 1555 1.95 LINK MG MG A 501 OD2 ASP B 252 1555 1555 2.58 LINK MG MG A 503 O1 ICT A 505 1555 1555 2.21 LINK MG MG A 503 O7 ICT A 505 1555 1555 2.21 LINK MG MG A 503 OD1 ASP B 275 1555 1555 2.22 SITE 1 AC1 4 ASP A 275 ASP A 279 ICT A 502 ASP B 252 SITE 1 AC2 13 THR A 77 SER A 94 ASN A 96 ARG A 100 SITE 2 AC2 13 ARG A 109 ARG A 132 TYR A 139 ASP A 275 SITE 3 AC2 13 MG A 501 HOH A 602 HOH A 614 LYS B 212 SITE 4 AC2 13 ASP B 252 SITE 1 AC3 3 ASP A 252 ICT A 505 ASP B 275 SITE 1 AC4 1 ICT A 505 SITE 1 AC5 12 LYS A 212 ASP A 252 MG A 503 K A 504 SITE 2 AC5 12 THR B 77 SER B 94 ASN B 96 ARG B 100 SITE 3 AC5 12 ARG B 109 ARG B 132 TYR B 139 ASP B 275 CRYST1 111.560 92.000 138.835 90.00 109.94 90.00 I 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 0.008964 0.000000 0.003251 0.00000 SCALE2 0.000000 0.010870 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007662 0.00000