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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
