HEADER OXIDOREDUCTASE 22-OCT-19 6L57 TITLE CRYSTAL STRUCTURE OF THE ALPHA GAMMA HETERODIMER OF HUMAN IDH3 IN TITLE 2 COMPLEX WITH CIT , MG AND ATP BINDING AT ALLOSTERIC SITE. 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 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: IDH3G; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TCA CYCLE, NAD-ISOCITRATE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.SUN,J.DING REVDAT 2 22-NOV-23 6L57 1 LINK REVDAT 1 29-APR-20 6L57 0 JRNL AUTH P.SUN,T.BAI,T.MA,J.DING JRNL TITL MOLECULAR MECHANISM OF THE DUAL REGULATORY ROLES OF ATP ON JRNL TITL 2 THE ALPHA GAMMA HETERODIMER OF HUMAN NAD-DEPENDENT JRNL TITL 3 ISOCITRATE DEHYDROGENASE. JRNL REF SCI REP V. 10 6225 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32277159 JRNL DOI 10.1038/S41598-020-63425-6 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 40991 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 2161 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 49.0570 - 5.6739 0.99 2770 133 0.1615 0.1787 REMARK 3 2 5.6739 - 4.5046 1.00 2649 148 0.1626 0.1831 REMARK 3 3 4.5046 - 3.9354 1.00 2627 147 0.1624 0.2055 REMARK 3 4 3.9354 - 3.5757 1.00 2568 164 0.1814 0.2065 REMARK 3 5 3.5757 - 3.3195 1.00 2632 120 0.2008 0.2395 REMARK 3 6 3.3195 - 3.1238 1.00 2601 143 0.2232 0.2773 REMARK 3 7 3.1238 - 2.9674 1.00 2532 155 0.2398 0.3075 REMARK 3 8 2.9674 - 2.8383 1.00 2548 182 0.2443 0.2734 REMARK 3 9 2.8383 - 2.7290 1.00 2555 165 0.2457 0.2862 REMARK 3 10 2.7290 - 2.6348 1.00 2559 142 0.2497 0.3163 REMARK 3 11 2.6348 - 2.5525 1.00 2561 129 0.2570 0.3071 REMARK 3 12 2.5525 - 2.4795 1.00 2575 138 0.2506 0.3096 REMARK 3 13 2.4795 - 2.4142 0.99 2513 154 0.2664 0.3061 REMARK 3 14 2.4142 - 2.3553 1.00 2560 144 0.2641 0.3099 REMARK 3 15 2.3553 - 2.3020 0.99 2580 97 0.2627 0.3071 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.94 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6L57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1300014200. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS 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) : 1 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41022 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 21.90 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 20.00 REMARK 200 R MERGE FOR SHELL (I) : 0.79700 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: PHENIX REMARK 200 STARTING MODEL: 5GRH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE, PH 8.0, AND 20% REMARK 280 (W/V) PEG3350, 2 MM ATP, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 299K 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 48.51567 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 97.03133 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 97.03133 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 48.51567 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: 5880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 524 LIES ON A SPECIAL POSITION. 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 -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 THR A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 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 MET B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 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 ILE B 347 REMARK 465 ASN B 348 REMARK 465 GLY B 349 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 LYS A 31 CG CD CE NZ REMARK 470 GLU A 56 CG CD OE1 OE2 REMARK 470 GLU A 59 CG CD OE1 OE2 REMARK 470 LYS A 63 CG CD CE NZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 THR A 74 OG1 CG2 REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 LEU A 314 CG CD1 CD2 REMARK 470 ASN A 321 CG OD1 ND2 REMARK 470 LYS A 323 CG CD CE NZ REMARK 470 GLU A 329 CG CD OE1 OE2 REMARK 470 LEU A 338 CG CD1 CD2 REMARK 470 ARG B 342 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 126 OD2 ASP A 230 2.10 REMARK 500 OE1 GLU A 202 O HOH A 501 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 268 NH1 ARG B 345 2445 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG B 345 NE ARG B 345 CZ 0.083 REMARK 500 REMARK 500 REMARK: NULL 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 ARG B 345 CB - CG - CD ANGL. DEV. = -16.6 DEGREES REMARK 500 ARG B 345 CG - CD - NE ANGL. DEV. = -12.6 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 37 73.12 -153.31 REMARK 500 LYS A 65 -47.67 73.35 REMARK 500 GLU A 123 -129.90 -130.20 REMARK 500 TYR A 126 38.96 -99.82 REMARK 500 HIS A 164 63.68 37.39 REMARK 500 MET A 177 71.12 -117.76 REMARK 500 CYS A 195 67.46 -111.51 REMARK 500 ASP A 220 -100.75 -123.35 REMARK 500 ARG B 72 -1.40 75.25 REMARK 500 THR B 117 -155.64 -117.54 REMARK 500 ASP B 123 86.77 -155.74 REMARK 500 GLU B 132 -157.73 -127.16 REMARK 500 ALA B 183 0.20 -64.64 REMARK 500 ASP B 229 -87.46 -127.25 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 O REMARK 620 2 ASP A 230 OD1 76.9 REMARK 620 3 ASP A 234 OD2 94.1 167.3 REMARK 620 4 ASP B 215 OD2 71.0 84.5 84.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 78 OD1 REMARK 620 2 ARG B 272 O 65.9 REMARK 620 3 HOH B 522 O 113.0 107.4 REMARK 620 4 HOH B 554 O 64.2 126.0 109.8 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 CIT B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ATP B 403 DBREF 6L57 A 1 339 UNP P50213 IDH3A_HUMAN 28 366 DBREF 6L57 B 1 354 UNP P51553 IDH3G_HUMAN 40 393 SEQADV 6L57 MET A -2 UNP P50213 INITIATING METHIONINE SEQADV 6L57 GLY A -1 UNP P50213 EXPRESSION TAG SEQADV 6L57 SER A 0 UNP P50213 EXPRESSION TAG SEQADV 6L57 MET B -2 UNP P51553 INITIATING METHIONINE SEQADV 6L57 GLY B -1 UNP P51553 EXPRESSION TAG SEQADV 6L57 SER B 0 UNP P51553 EXPRESSION TAG SEQRES 1 A 342 MET GLY SER THR GLY GLY VAL GLN THR VAL THR LEU ILE SEQRES 2 A 342 PRO GLY ASP GLY ILE GLY PRO GLU ILE SER ALA ALA VAL SEQRES 3 A 342 MET LYS ILE PHE ASP ALA ALA LYS ALA PRO ILE GLN TRP SEQRES 4 A 342 GLU GLU ARG ASN VAL THR ALA ILE GLN GLY PRO GLY GLY SEQRES 5 A 342 LYS TRP MET ILE PRO SER GLU ALA LYS GLU SER MET ASP SEQRES 6 A 342 LYS ASN LYS MET GLY LEU LYS GLY PRO LEU LYS THR PRO SEQRES 7 A 342 ILE ALA ALA GLY HIS PRO SER MET ASN LEU LEU LEU ARG SEQRES 8 A 342 LYS THR PHE ASP LEU TYR ALA ASN VAL ARG PRO CYS VAL SEQRES 9 A 342 SER ILE GLU GLY TYR LYS THR PRO TYR THR ASP VAL ASN SEQRES 10 A 342 ILE VAL THR ILE ARG GLU ASN THR GLU GLY GLU TYR SER SEQRES 11 A 342 GLY ILE GLU HIS VAL ILE VAL ASP GLY VAL VAL GLN SER SEQRES 12 A 342 ILE LYS LEU ILE THR GLU GLY ALA SER LYS ARG ILE ALA SEQRES 13 A 342 GLU PHE ALA PHE GLU TYR ALA ARG ASN ASN HIS ARG SER SEQRES 14 A 342 ASN VAL THR ALA VAL HIS LYS ALA ASN ILE MET ARG MET SEQRES 15 A 342 SER ASP GLY LEU PHE LEU GLN LYS CYS ARG GLU VAL ALA SEQRES 16 A 342 GLU SER CYS LYS ASP ILE LYS PHE ASN GLU MET TYR LEU SEQRES 17 A 342 ASP THR VAL CYS LEU ASN MET VAL GLN ASP PRO SER GLN SEQRES 18 A 342 PHE ASP VAL LEU VAL MET PRO ASN LEU TYR GLY ASP ILE SEQRES 19 A 342 LEU SER ASP LEU CYS ALA GLY LEU ILE GLY GLY LEU GLY SEQRES 20 A 342 VAL THR PRO SER GLY ASN ILE GLY ALA ASN GLY VAL ALA SEQRES 21 A 342 ILE PHE GLU SER VAL HIS GLY THR ALA PRO ASP ILE ALA SEQRES 22 A 342 GLY LYS ASP MET ALA ASN PRO THR ALA LEU LEU LEU SER SEQRES 23 A 342 ALA VAL MET MET LEU ARG HIS MET GLY LEU PHE ASP HIS SEQRES 24 A 342 ALA ALA ARG ILE GLU ALA ALA CYS PHE ALA THR ILE LYS SEQRES 25 A 342 ASP GLY LYS SER LEU THR LYS ASP LEU GLY GLY ASN ALA SEQRES 26 A 342 LYS CYS SER ASP PHE THR GLU GLU ILE CYS ARG ARG VAL SEQRES 27 A 342 LYS ASP LEU ASP SEQRES 1 B 357 MET GLY SER PHE SER GLU GLN THR ILE PRO PRO SER ALA SEQRES 2 B 357 LYS TYR GLY GLY ARG HIS THR VAL THR MET ILE PRO GLY SEQRES 3 B 357 ASP GLY ILE GLY PRO GLU LEU MET LEU HIS VAL LYS SER SEQRES 4 B 357 VAL PHE ARG HIS ALA CYS VAL PRO VAL ASP PHE GLU GLU SEQRES 5 B 357 VAL HIS VAL SER SER ASN ALA ASP GLU GLU ASP ILE ARG SEQRES 6 B 357 ASN ALA ILE MET ALA ILE ARG ARG ASN ARG VAL ALA LEU SEQRES 7 B 357 LYS GLY ASN ILE GLU THR ASN HIS ASN LEU PRO PRO SER SEQRES 8 B 357 HIS LYS SER ARG ASN ASN ILE LEU ARG THR SER LEU ASP SEQRES 9 B 357 LEU TYR ALA ASN VAL ILE HIS CYS LYS SER LEU PRO GLY SEQRES 10 B 357 VAL VAL THR ARG HIS LYS ASP ILE ASP ILE LEU ILE VAL SEQRES 11 B 357 ARG GLU ASN THR GLU GLY GLU TYR SER SER LEU GLU HIS SEQRES 12 B 357 GLU SER VAL ALA GLY VAL VAL GLU SER LEU LYS ILE ILE SEQRES 13 B 357 THR LYS ALA LYS SER LEU ARG ILE ALA GLU TYR ALA PHE SEQRES 14 B 357 LYS LEU ALA GLN GLU SER GLY ARG LYS LYS VAL THR ALA SEQRES 15 B 357 VAL HIS LYS ALA ASN ILE MET LYS LEU GLY ASP GLY LEU SEQRES 16 B 357 PHE LEU GLN CYS CYS ARG GLU VAL ALA ALA ARG TYR PRO SEQRES 17 B 357 GLN ILE THR PHE GLU ASN MET ILE VAL ASP ASN THR THR SEQRES 18 B 357 MET GLN LEU VAL SER ARG PRO GLN GLN PHE ASP VAL MET SEQRES 19 B 357 VAL MET PRO ASN LEU TYR GLY ASN ILE VAL ASN ASN VAL SEQRES 20 B 357 CYS ALA GLY LEU VAL GLY GLY PRO GLY LEU VAL ALA GLY SEQRES 21 B 357 ALA ASN TYR GLY HIS VAL TYR ALA VAL PHE GLU THR ALA SEQRES 22 B 357 THR ARG ASN THR GLY LYS SER ILE ALA ASN LYS ASN ILE SEQRES 23 B 357 ALA ASN PRO THR ALA THR LEU LEU ALA SER CYS MET MET SEQRES 24 B 357 LEU ASP HIS LEU LYS LEU HIS SER TYR ALA THR SER ILE SEQRES 25 B 357 ARG LYS ALA VAL LEU ALA SER MET ASP ASN GLU ASN MET SEQRES 26 B 357 HIS THR PRO ASP ILE GLY GLY GLN GLY THR THR SER GLU SEQRES 27 B 357 ALA ILE GLN ASP VAL ILE ARG HIS ILE ARG VAL ILE ASN SEQRES 28 B 357 GLY ARG ALA VAL GLU ALA HET MG A 401 1 HET CIT B 401 13 HET MG B 402 1 HET ATP B 403 31 HETNAM MG MAGNESIUM ION HETNAM CIT CITRIC ACID HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 3 MG 2(MG 2+) FORMUL 4 CIT C6 H8 O7 FORMUL 6 ATP C10 H16 N5 O13 P3 FORMUL 7 HOH *125(H2 O) 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 123 SER A 127 5 5 HELIX 5 AA5 GLU A 146 ASN A 163 1 18 HELIX 6 AA6 MET A 179 CYS A 195 1 17 HELIX 7 AA7 LEU A 205 VAL A 213 1 9 HELIX 8 AA8 ASP A 215 PHE A 219 5 5 HELIX 9 AA9 PRO A 225 ILE A 240 1 16 HELIX 10 AB1 GLY A 242 THR A 246 5 5 HELIX 11 AB2 PRO A 277 GLY A 292 1 16 HELIX 12 AB3 LEU A 293 GLY A 311 1 19 HELIX 13 AB4 THR A 315 GLY A 319 5 5 HELIX 14 AB5 LYS A 323 LEU A 338 1 16 HELIX 15 AB6 ILE B 26 ALA B 41 1 16 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 SER B 172 1 18 HELIX 20 AC2 LEU B 188 ALA B 202 1 15 HELIX 21 AC3 VAL B 214 VAL B 222 1 9 HELIX 22 AC4 ARG B 224 PHE B 228 5 5 HELIX 23 AC5 PRO B 234 GLY B 250 1 17 HELIX 24 AC6 GLY B 275 ALA B 279 5 5 HELIX 25 AC7 PRO B 286 LEU B 300 1 15 HELIX 26 AC8 LEU B 302 ASN B 319 1 18 HELIX 27 AC9 GLU B 320 HIS B 323 5 4 HELIX 28 AD1 THR B 324 GLY B 328 5 5 HELIX 29 AD2 THR B 332 ILE B 344 1 13 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 GLU A 260 1 O PHE A 259 N LYS A 69 SHEET 5 AA110 GLY A 249 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 LYS A 199 N VAL A 168 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 GLU B 141 -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 VAL B 18 O GLU B 48 SHEET 3 AA310 VAL B 73 LYS B 76 1 O VAL B 73 N THR B 19 SHEET 4 AA310 ALA B 265 THR B 269 1 O PHE B 267 N LYS B 76 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 ARG B 128 N ASN B 105 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 230 SHEET 10 AA310 THR B 208 ILE B 213 1 O THR B 208 N VAL B 177 LINK O ASP A 230 MG MG A 401 1555 1555 2.90 LINK OD1 ASP A 230 MG MG A 401 1555 1555 2.52 LINK OD2 ASP A 234 MG MG A 401 1555 1555 2.56 LINK MG MG A 401 OD2 ASP B 215 1555 1555 2.20 LINK OD1 ASN B 78 MG MG B 402 1555 1555 2.76 LINK O ARG B 272 MG MG B 402 1555 1555 2.58 LINK MG MG B 402 O HOH B 522 1555 1555 2.81 LINK MG MG B 402 O HOH B 554 1555 1555 2.75 CISPEP 1 ASP A 310 GLY A 311 0 -5.88 SITE 1 AC1 4 ASP A 230 ASP A 234 HOH A 511 ASP B 215 SITE 1 AC2 13 LYS A 173 ASN A 175 ASN B 78 THR B 81 SITE 2 AC2 13 SER B 91 ASN B 93 ARG B 97 ARG B 128 SITE 3 AC2 13 TYR B 135 ASN B 239 ARG B 272 MG B 402 SITE 4 AC2 13 HOH B 554 SITE 1 AC3 5 ASN B 78 ARG B 272 CIT B 401 HOH B 522 SITE 2 AC3 5 HOH B 554 SITE 1 AC4 13 ILE B 26 PRO B 252 ASN B 273 THR B 274 SITE 2 AC4 13 GLY B 275 LYS B 276 SER B 277 ILE B 278 SITE 3 AC4 13 ALA B 284 ASN B 285 ASP B 326 HOH B 521 SITE 4 AC4 13 HOH B 522 CRYST1 104.211 104.211 145.547 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 0.009596 0.005540 0.000000 0.00000 SCALE2 0.000000 0.011080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006871 0.00000