PDB Short entry for 5GRL HEADER OXIDOREDUCTASE 11-AUG-16 5GRL TITLE CRYSTAL STRUCTURE OF THE ALPHA GAMMA HETERODIMER OF HUMAN IDH3 IN TITLE 2 COMPLEX WITH MG(2+), ISOCITRATE AND ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, COMPND 3 MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: ISOCITRIC DEHYDROGENASE SUBUNIT ALPHA,NAD(+)-SPECIFIC ICDH COMPND 6 SUBUNIT ALPHA; COMPND 7 EC: 1.1.1.41; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT GAMMA, COMPND 11 MITOCHONDRIAL; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: ISOCITRIC DEHYDROGENASE SUBUNIT GAMMA,NAD(+)-SPECIFIC ICDH COMPND 14 SUBUNIT GAMMA; COMPND 15 EC: 1.1.1.41; COMPND 16 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: IDH3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: IDH3G; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ALLOSTERIC REGULATION, ISOCITRATE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.MA,J.DING REVDAT 3 08-NOV-23 5GRL 1 LINK REVDAT 2 04-OCT-17 5GRL 1 REMARK REVDAT 1 15-FEB-17 5GRL 0 JRNL AUTH T.MA,Y.PENG,W.HUANG,J.DING JRNL TITL MOLECULAR MECHANISM OF THE ALLOSTERIC REGULATION OF THE JRNL TITL 2 ALPHA GAMMA HETERODIMER OF HUMAN NAD-DEPENDENT ISOCITRATE JRNL TITL 3 DEHYDROGENASE. JRNL REF SCI REP V. 7 40921 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28098230 JRNL DOI 10.1038/SREP40921 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 24151 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) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1284 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) : 2.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1419 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3190 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5035 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.08000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.27000 REMARK 3 B12 (A**2) : 0.04000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.748 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.361 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.300 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.599 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.896 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.851 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5154 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5025 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6971 ; 1.110 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11555 ; 0.880 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 653 ; 5.703 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 217 ;38.088 ;24.470 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 913 ;15.663 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.844 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 812 ; 0.057 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5800 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1119 ; 0.001 ; 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): 2627 ; 2.267 ; 3.898 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2626 ; 2.262 ; 3.897 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3275 ; 3.654 ; 5.827 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 REMARK 4 REMARK 4 5GRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1300001317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 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 : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25878 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5GRI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES-NA, PH 7.5, 12% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.49267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 96.98533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 96.98533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 48.49267 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: 5950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 THR A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 GLY A 46 REMARK 465 PRO A 47 REMARK 465 GLY A 48 REMARK 465 GLY A 49 REMARK 465 LYS A 50 REMARK 465 PRO A 75 REMARK 465 ILE A 76 REMARK 465 ALA A 77 REMARK 465 ALA A 78 REMARK 465 GLY A 79 REMARK 465 HIS A 80 REMARK 465 LEU A 318 REMARK 465 ASP A 339 REMARK 465 PHE B 1 REMARK 465 SER B 2 REMARK 465 GLU B 3 REMARK 465 GLN B 4 REMARK 465 THR B 5 REMARK 465 ILE B 6 REMARK 465 PRO B 7 REMARK 465 PRO B 8 REMARK 465 SER B 9 REMARK 465 ALA B 10 REMARK 465 LYS B 11 REMARK 465 TYR B 12 REMARK 465 GLY B 13 REMARK 465 GLY B 14 REMARK 465 ARG B 350 REMARK 465 ALA B 351 REMARK 465 VAL B 352 REMARK 465 GLU B 353 REMARK 465 ALA B 354 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 GLN A 45 CG CD OE1 NE2 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 THR A 42 145.50 -171.95 REMARK 500 LYS A 65 -3.93 71.10 REMARK 500 ASN A 114 79.67 -159.53 REMARK 500 GLU A 123 -145.24 -137.70 REMARK 500 TYR A 126 53.46 -98.14 REMARK 500 MET A 177 77.39 -102.36 REMARK 500 CYS A 195 58.64 -140.10 REMARK 500 ASP A 220 -75.62 -127.62 REMARK 500 ASN A 254 56.56 38.39 REMARK 500 ARG B 72 -4.01 72.10 REMARK 500 ASP B 123 82.38 -158.71 REMARK 500 GLU B 132 -159.64 -142.35 REMARK 500 ASP B 229 -95.19 -129.83 REMARK 500 PRO B 234 -179.35 -64.73 REMARK 500 LEU B 302 54.46 -97.41 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 230 OD1 REMARK 620 2 ASP A 234 OD1 119.6 REMARK 620 3 ASP B 215 OD2 76.9 111.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 78 OD1 REMARK 620 2 ARG B 272 O 73.8 REMARK 620 3 ADP B 401 O2B 85.9 89.8 REMARK 620 4 ICT B 402 O4 97.2 84.8 172.7 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ICT B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GRH RELATED DB: PDB REMARK 900 RELATED ID: 5GRI RELATED DB: PDB REMARK 900 RELATED ID: 5GRF RELATED DB: PDB REMARK 900 RELATED ID: 5GRE RELATED DB: PDB DBREF 5GRL A 1 339 UNP P50213 IDH3A_HUMAN 28 366 DBREF 5GRL B 1 354 UNP P51553 IDH3G_HUMAN 40 393 SEQRES 1 A 339 THR GLY GLY VAL GLN THR VAL THR LEU ILE PRO GLY ASP SEQRES 2 A 339 GLY ILE GLY PRO GLU ILE SER ALA ALA VAL MET LYS ILE SEQRES 3 A 339 PHE ASP ALA ALA LYS ALA PRO ILE GLN TRP GLU GLU ARG SEQRES 4 A 339 ASN VAL THR ALA ILE GLN GLY PRO GLY GLY LYS TRP MET SEQRES 5 A 339 ILE PRO SER GLU ALA LYS GLU SER MET ASP LYS ASN LYS SEQRES 6 A 339 MET GLY LEU LYS GLY PRO LEU LYS THR PRO ILE ALA ALA SEQRES 7 A 339 GLY HIS PRO SER MET ASN LEU LEU LEU ARG LYS THR PHE SEQRES 8 A 339 ASP LEU TYR ALA ASN VAL ARG PRO CYS VAL SER ILE GLU SEQRES 9 A 339 GLY TYR LYS THR PRO TYR THR ASP VAL ASN ILE VAL THR SEQRES 10 A 339 ILE ARG GLU ASN THR GLU GLY GLU TYR SER GLY ILE GLU SEQRES 11 A 339 HIS VAL ILE VAL ASP GLY VAL VAL GLN SER ILE LYS LEU SEQRES 12 A 339 ILE THR GLU GLY ALA SER LYS ARG ILE ALA GLU PHE ALA SEQRES 13 A 339 PHE GLU TYR ALA ARG ASN ASN HIS ARG SER ASN VAL THR SEQRES 14 A 339 ALA VAL HIS LYS ALA ASN ILE MET ARG MET SER ASP GLY SEQRES 15 A 339 LEU PHE LEU GLN LYS CYS ARG GLU VAL ALA GLU SER CYS SEQRES 16 A 339 LYS ASP ILE LYS PHE ASN GLU MET TYR LEU ASP THR VAL SEQRES 17 A 339 CYS LEU ASN MET VAL GLN ASP PRO SER GLN PHE ASP VAL SEQRES 18 A 339 LEU VAL MET PRO ASN LEU TYR GLY ASP ILE LEU SER ASP SEQRES 19 A 339 LEU CYS ALA GLY LEU ILE GLY GLY LEU GLY VAL THR PRO SEQRES 20 A 339 SER GLY ASN ILE GLY ALA ASN GLY VAL ALA ILE PHE GLU SEQRES 21 A 339 SER VAL HIS GLY THR ALA PRO ASP ILE ALA GLY LYS ASP SEQRES 22 A 339 MET ALA ASN PRO THR ALA LEU LEU LEU SER ALA VAL MET SEQRES 23 A 339 MET LEU ARG HIS MET GLY LEU PHE ASP HIS ALA ALA ARG SEQRES 24 A 339 ILE GLU ALA ALA CYS PHE ALA THR ILE LYS ASP GLY LYS SEQRES 25 A 339 SER LEU THR LYS ASP LEU GLY GLY ASN ALA LYS CYS SER SEQRES 26 A 339 ASP PHE THR GLU GLU ILE CYS ARG ARG VAL LYS ASP LEU SEQRES 27 A 339 ASP SEQRES 1 B 354 PHE SER GLU GLN THR ILE PRO PRO SER ALA LYS TYR GLY SEQRES 2 B 354 GLY ARG HIS THR VAL THR MET ILE PRO GLY ASP GLY ILE SEQRES 3 B 354 GLY PRO GLU LEU MET LEU HIS VAL LYS SER VAL PHE ARG SEQRES 4 B 354 HIS ALA CYS VAL PRO VAL ASP PHE GLU GLU VAL HIS VAL SEQRES 5 B 354 SER SER ASN ALA ASP GLU GLU ASP ILE ARG ASN ALA ILE SEQRES 6 B 354 MET ALA ILE ARG ARG ASN ARG VAL ALA LEU LYS GLY ASN SEQRES 7 B 354 ILE GLU THR ASN HIS ASN LEU PRO PRO SER HIS LYS SER SEQRES 8 B 354 ARG ASN ASN ILE LEU ARG THR SER LEU ASP LEU TYR ALA SEQRES 9 B 354 ASN VAL ILE HIS CYS LYS SER LEU PRO GLY VAL VAL THR SEQRES 10 B 354 ARG HIS LYS ASP ILE ASP ILE LEU ILE VAL ARG GLU ASN SEQRES 11 B 354 THR GLU GLY GLU TYR SER SER LEU GLU HIS GLU SER VAL SEQRES 12 B 354 ALA GLY VAL VAL GLU SER LEU LYS ILE ILE THR LYS ALA SEQRES 13 B 354 LYS SER LEU ARG ILE ALA GLU TYR ALA PHE LYS LEU ALA SEQRES 14 B 354 GLN GLU SER GLY ARG LYS LYS VAL THR ALA VAL HIS LYS SEQRES 15 B 354 ALA ASN ILE MET LYS LEU GLY ASP GLY LEU PHE LEU GLN SEQRES 16 B 354 CYS CYS ARG GLU VAL ALA ALA ARG TYR PRO GLN ILE THR SEQRES 17 B 354 PHE GLU ASN MET ILE VAL ASP ASN THR THR MET GLN LEU SEQRES 18 B 354 VAL SER ARG PRO GLN GLN PHE ASP VAL MET VAL MET PRO SEQRES 19 B 354 ASN LEU TYR GLY ASN ILE VAL ASN ASN VAL CYS ALA GLY SEQRES 20 B 354 LEU VAL GLY GLY PRO GLY LEU VAL ALA GLY ALA ASN TYR SEQRES 21 B 354 GLY HIS VAL TYR ALA VAL PHE GLU THR ALA THR ARG ASN SEQRES 22 B 354 THR GLY LYS SER ILE ALA ASN LYS ASN ILE ALA ASN PRO SEQRES 23 B 354 THR ALA THR LEU LEU ALA SER CYS MET MET LEU ASP HIS SEQRES 24 B 354 LEU LYS LEU HIS SER TYR ALA THR SER ILE ARG LYS ALA SEQRES 25 B 354 VAL LEU ALA SER MET ASP ASN GLU ASN MET HIS THR PRO SEQRES 26 B 354 ASP ILE GLY GLY GLN GLY THR THR SER GLU ALA ILE GLN SEQRES 27 B 354 ASP VAL ILE ARG HIS ILE ARG VAL ILE ASN GLY ARG ALA SEQRES 28 B 354 VAL GLU ALA HET MG A 401 1 HET ADP B 401 27 HET ICT B 402 13 HET MG B 403 1 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM ICT ISOCITRIC ACID FORMUL 3 MG 2(MG 2+) FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 ICT C6 H8 O7 HELIX 1 AA1 ILE A 15 ALA A 30 1 16 HELIX 2 AA2 PRO A 54 LYS A 65 1 12 HELIX 3 AA3 SER A 82 ASP A 92 1 11 HELIX 4 AA4 GLU A 146 ASN A 163 1 18 HELIX 5 AA5 MET A 177 SER A 194 1 18 HELIX 6 AA6 LEU A 205 VAL A 213 1 9 HELIX 7 AA7 ASP A 215 PHE A 219 5 5 HELIX 8 AA8 PRO A 225 GLY A 241 1 17 HELIX 9 AA9 GLY A 242 VAL A 245 5 4 HELIX 10 AB1 ALA A 253 GLY A 255 5 3 HELIX 11 AB2 ALA A 266 ALA A 270 5 5 HELIX 12 AB3 PRO A 277 GLY A 292 1 16 HELIX 13 AB4 LEU A 293 GLY A 311 1 19 HELIX 14 AB5 LYS A 323 ASP A 337 1 15 HELIX 15 AB6 ILE B 26 CYS B 42 1 17 HELIX 16 AB7 GLU B 58 ARG B 72 1 15 HELIX 17 AB8 SER B 91 LEU B 100 1 10 HELIX 18 AB9 GLU B 132 SER B 136 5 5 HELIX 19 AC1 LYS B 155 GLY B 173 1 19 HELIX 20 AC2 LEU B 188 ALA B 202 1 15 HELIX 21 AC3 VAL B 214 ARG B 224 1 11 HELIX 22 AC4 PRO B 225 PHE B 228 5 4 HELIX 23 AC5 PRO B 234 VAL B 249 1 16 HELIX 24 AC6 PRO B 286 LEU B 300 1 15 HELIX 25 AC7 LEU B 302 ASN B 319 1 18 HELIX 26 AC8 GLU B 320 HIS B 323 5 4 HELIX 27 AC9 THR B 324 GLY B 328 5 5 HELIX 28 AD1 THR B 332 GLY B 349 1 18 SHEET 1 AA110 ILE A 34 GLU A 38 0 SHEET 2 AA110 GLN A 5 ILE A 10 1 N VAL A 7 O GLN A 35 SHEET 3 AA110 MET A 66 LYS A 69 1 O LEU A 68 N ILE A 10 SHEET 4 AA110 ALA A 257 SER A 261 1 O SER A 261 N LYS A 69 SHEET 5 AA110 PRO A 247 ILE A 251 -1 N ASN A 250 O ILE A 258 SHEET 6 AA110 ALA A 95 VAL A 101 -1 N VAL A 97 O GLY A 249 SHEET 7 AA110 ASN A 114 GLU A 120 -1 O ILE A 115 N CYS A 100 SHEET 8 AA110 VAL A 221 MET A 224 1 O LEU A 222 N ILE A 118 SHEET 9 AA110 ASN A 167 HIS A 172 1 N THR A 169 O VAL A 221 SHEET 10 AA110 LYS A 199 TYR A 204 1 O ASN A 201 N ALA A 170 SHEET 1 AA2 4 GLU A 130 VAL A 134 0 SHEET 2 AA2 4 VAL A 137 THR A 145 -1 O GLN A 139 N HIS A 131 SHEET 3 AA2 4 VAL B 146 THR B 154 -1 O ILE B 153 N VAL A 138 SHEET 4 AA2 4 GLU B 139 VAL B 143 -1 N HIS B 140 O GLU B 148 SHEET 1 AA310 VAL B 45 GLU B 49 0 SHEET 2 AA310 HIS B 16 ILE B 21 1 N HIS B 16 O ASP B 46 SHEET 3 AA310 VAL B 73 LYS B 76 1 O LEU B 75 N THR B 19 SHEET 4 AA310 ALA B 265 THR B 269 1 O PHE B 267 N ALA B 74 SHEET 5 AA310 ALA B 256 TYR B 260 -1 N GLY B 257 O GLU B 268 SHEET 6 AA310 ALA B 104 LYS B 110 -1 N ALA B 104 O TYR B 260 SHEET 7 AA310 ASP B 123 GLU B 129 -1 O ILE B 126 N ILE B 107 SHEET 8 AA310 VAL B 230 MET B 233 1 O MET B 231 N VAL B 127 SHEET 9 AA310 LYS B 176 HIS B 181 1 N THR B 178 O VAL B 232 SHEET 10 AA310 THR B 208 ILE B 213 1 O THR B 208 N VAL B 177 LINK OD1 ASP A 230 MG MG A 401 1555 1555 2.25 LINK OD1 ASP A 234 MG MG A 401 1555 1555 2.91 LINK MG MG A 401 OD2 ASP B 215 1555 1555 2.31 LINK OD1 ASN B 78 MG MG B 403 1555 1555 2.40 LINK O ARG B 272 MG MG B 403 1555 1555 2.51 LINK O2B ADP B 401 MG MG B 403 1555 1555 2.27 LINK O4 ICT B 402 MG MG B 403 1555 1555 2.47 SITE 1 AC1 3 ASP A 230 ASP A 234 ASP B 215 SITE 1 AC2 14 TYR A 204 ILE B 26 ASN B 78 PRO B 252 SITE 2 AC2 14 ARG B 272 ASN B 273 THR B 274 GLY B 275 SITE 3 AC2 14 LYS B 276 SER B 277 ILE B 278 ASN B 285 SITE 4 AC2 14 ASP B 326 MG B 403 SITE 1 AC3 12 LYS A 173 ASN A 175 ILE A 176 ASN B 78 SITE 2 AC3 12 SER B 91 ASN B 93 ARG B 97 ARG B 128 SITE 3 AC3 12 TYR B 135 ASN B 239 ARG B 272 MG B 403 SITE 1 AC4 4 ASN B 78 ARG B 272 ADP B 401 ICT B 402 CRYST1 111.238 111.238 145.478 90.00 90.00 120.00 P 31 2 1 6 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 0.008990 0.005190 0.000000 0.00000 SCALE2 0.000000 0.010380 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006874 0.00000