HEADER OXIDOREDUCTASE 23-OCT-16 5H3E TITLE CRYSTAL STRUCTURE OF MOUSE ISOCITRATE DEHYDROGENASES 2 K256Q MUTANT TITLE 2 COMPLEXED WITH ISOCITRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP], MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ISOCITRATE DEHYDROGENASE 2; COMPND 5 EC: 1.1.1.42; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 ORGAN: LIVER; SOURCE 6 GENE: IDH2; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: KRX; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-26B(+) KEYWDS NADP DEPENDENT ISOCITRATE DEHYDROGENASES 2, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,L.LIU,T.MIYAKAWA,A.NAKAMURA,M.TANOKURA REVDAT 3 08-NOV-23 5H3E 1 LINK REVDAT 2 13-SEP-17 5H3E 1 JRNL REVDAT 1 30-AUG-17 5H3E 0 JRNL AUTH Y.XU,L.LIU,A.NAKAMURA,S.SOMEYA,T.MIYAKAWA,M.TANOKURA JRNL TITL STUDIES ON THE REGULATORY MECHANISM OF ISOCITRATE JRNL TITL 2 DEHYDROGENASE 2 USING ACETYLATION MIMICS JRNL REF SCI REP V. 7 9785 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28852116 JRNL DOI 10.1038/S41598-017-10337-7 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 36284 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1874 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) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2131 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 119 REMARK 3 BIN FREE R VALUE : 0.2280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6507 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 128 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 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): 0.394 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.236 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.348 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6679 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6363 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9023 ; 1.080 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14667 ; 0.847 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 817 ; 5.977 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 304 ;33.696 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1180 ;14.622 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.775 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 985 ; 0.061 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7517 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1551 ; 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): 3274 ; 0.641 ; 3.198 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3273 ; 0.641 ; 3.197 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4089 ; 1.128 ; 4.794 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4090 ; 1.128 ; 4.795 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3405 ; 0.530 ; 3.264 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3403 ; 0.530 ; 3.264 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4934 ; 0.942 ; 4.858 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7433 ; 2.503 ;24.972 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7423 ; 2.497 ;24.950 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 REMARK 4 REMARK 4 5H3E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37204 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 45.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 4L04 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M AMMONIUM FORMATE, 24%(W/V) PEG REMARK 280 3350, PH 6.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,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 137.94333 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 68.97167 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: 8630 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 39 REMARK 465 ALA A 40 REMARK 465 GLU A 41 REMARK 465 LYS A 451 REMARK 465 GLN A 452 REMARK 465 LEU A 453 REMARK 465 GLU A 454 REMARK 465 HIS A 455 REMARK 465 HIS A 456 REMARK 465 HIS A 457 REMARK 465 HIS A 458 REMARK 465 HIS A 459 REMARK 465 HIS A 460 REMARK 465 MET B 39 REMARK 465 ALA B 40 REMARK 465 GLU B 41 REMARK 465 GLN B 452 REMARK 465 LEU B 453 REMARK 465 GLU B 454 REMARK 465 HIS B 455 REMARK 465 HIS B 456 REMARK 465 HIS B 457 REMARK 465 HIS B 458 REMARK 465 HIS B 459 REMARK 465 HIS B 460 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 194 CD2 REMARK 470 ASP A 271 OD2 REMARK 470 THR A 435 CG2 REMARK 470 LEU B 194 CD1 REMARK 470 ASP B 271 OD2 REMARK 470 THR B 435 CG2 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 57 -127.73 52.67 REMARK 500 SER A 108 -5.19 79.71 REMARK 500 ASP A 119 -163.85 -118.32 REMARK 500 TRP A 164 83.05 -69.87 REMARK 500 ASP A 177 -130.28 57.84 REMARK 500 ALA A 214 -155.77 -137.24 REMARK 500 GLU A 429 -58.43 -131.12 REMARK 500 GLU B 57 -134.46 54.42 REMARK 500 ILE B 71 -72.66 -93.71 REMARK 500 ASP B 119 -150.53 -121.81 REMARK 500 ASP B 177 -133.37 56.82 REMARK 500 ALA B 214 -156.52 -134.86 REMARK 500 LEU B 329 64.76 -109.12 REMARK 500 LYS B 340 -46.52 -138.51 REMARK 500 SER B 365 80.24 -151.85 REMARK 500 ASN B 428 -4.03 65.83 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 B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 291 OD2 REMARK 620 2 ASP B 314 OD1 85.5 REMARK 620 3 ICT B 502 O7 69.1 79.7 REMARK 620 4 ICT B 502 O1 131.1 81.6 62.2 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 314 OD1 REMARK 620 2 ICT A 502 O2 83.7 REMARK 620 3 ICT A 502 O7 89.4 67.9 REMARK 620 4 ASP B 291 OD2 95.0 148.4 80.5 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 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ICT B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H3F RELATED DB: PDB DBREF 5H3E A 40 452 UNP P54071 IDHP_MOUSE 40 452 DBREF 5H3E B 40 452 UNP P54071 IDHP_MOUSE 40 452 SEQADV 5H3E MET A 39 UNP P54071 EXPRESSION TAG SEQADV 5H3E GLN A 256 UNP P54071 LYS 256 ENGINEERED MUTATION SEQADV 5H3E LEU A 453 UNP P54071 EXPRESSION TAG SEQADV 5H3E GLU A 454 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS A 455 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS A 456 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS A 457 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS A 458 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS A 459 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS A 460 UNP P54071 EXPRESSION TAG SEQADV 5H3E MET B 39 UNP P54071 EXPRESSION TAG SEQADV 5H3E GLN B 256 UNP P54071 LYS 256 ENGINEERED MUTATION SEQADV 5H3E LEU B 453 UNP P54071 EXPRESSION TAG SEQADV 5H3E GLU B 454 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS B 455 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS B 456 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS B 457 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS B 458 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS B 459 UNP P54071 EXPRESSION TAG SEQADV 5H3E HIS B 460 UNP P54071 EXPRESSION TAG SEQRES 1 A 422 MET ALA GLU LYS ARG ILE LYS VAL GLU LYS PRO VAL VAL SEQRES 2 A 422 GLU MET ASP GLY ASP GLU MET THR ARG ILE ILE TRP GLN SEQRES 3 A 422 PHE ILE LYS GLU LYS LEU ILE LEU PRO HIS VAL ASP VAL SEQRES 4 A 422 GLN LEU LYS TYR PHE ASP LEU GLY LEU PRO ASN ARG ASP SEQRES 5 A 422 GLN THR ASN ASP GLN VAL THR ILE ASP SER ALA LEU ALA SEQRES 6 A 422 THR GLN LYS TYR SER VAL ALA VAL LYS CYS ALA THR ILE SEQRES 7 A 422 THR PRO ASP GLU ALA ARG VAL GLU GLU PHE LYS LEU LYS SEQRES 8 A 422 LYS MET TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE SEQRES 9 A 422 LEU GLY GLY THR VAL PHE ARG GLU PRO ILE ILE CYS LYS SEQRES 10 A 422 ASN ILE PRO ARG LEU VAL PRO GLY TRP THR LYS PRO ILE SEQRES 11 A 422 THR ILE GLY ARG HIS ALA HIS GLY ASP GLN TYR LYS ALA SEQRES 12 A 422 THR ASP PHE VAL VAL ASP ARG ALA GLY THR PHE LYS LEU SEQRES 13 A 422 VAL PHE THR PRO LYS ASP GLY SER SER ALA LYS GLU TRP SEQRES 14 A 422 GLU VAL TYR ASN PHE PRO ALA GLY GLY VAL GLY MET GLY SEQRES 15 A 422 MET TYR ASN THR ASP GLU SER ILE SER GLY PHE ALA HIS SEQRES 16 A 422 SER CYS PHE GLN TYR SER ILE GLN LYS LYS TRP PRO LEU SEQRES 17 A 422 TYR LEU SER THR LYS ASN THR ILE LEU GLN ALA TYR ASP SEQRES 18 A 422 GLY ARG PHE LYS ASP ILE PHE GLN GLU ILE PHE ASP LYS SEQRES 19 A 422 HIS TYR LYS THR ASP PHE ASP LYS ASN LYS ILE TRP TYR SEQRES 20 A 422 GLU HIS ARG LEU ILE ASP ASP MET VAL ALA GLN VAL LEU SEQRES 21 A 422 LYS SER SER GLY GLY PHE VAL TRP ALA CYS LYS ASN TYR SEQRES 22 A 422 ASP GLY ASP VAL GLN SER ASP ILE LEU ALA GLN GLY PHE SEQRES 23 A 422 GLY SER LEU GLY LEU MET THR SER VAL LEU VAL CYS PRO SEQRES 24 A 422 ASP GLY LYS THR ILE GLU ALA GLU ALA ALA HIS GLY THR SEQRES 25 A 422 VAL THR ARG HIS TYR ARG GLU HIS GLN LYS GLY ARG PRO SEQRES 26 A 422 THR SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR SEQRES 27 A 422 ARG GLY LEU GLU HIS ARG GLY LYS LEU ASP GLY ASN GLN SEQRES 28 A 422 ASP LEU ILE ARG PHE ALA GLN THR LEU GLU LYS VAL CYS SEQRES 29 A 422 VAL GLN THR VAL GLU SER GLY ALA MET THR LYS ASP LEU SEQRES 30 A 422 ALA GLY CYS ILE HIS GLY LEU SER ASN VAL LYS LEU ASN SEQRES 31 A 422 GLU HIS PHE LEU ASN THR THR ASP PHE LEU ASP THR ILE SEQRES 32 A 422 LYS SER ASN LEU ASP ARG ALA LEU GLY LYS GLN LEU GLU SEQRES 33 A 422 HIS HIS HIS HIS HIS HIS SEQRES 1 B 422 MET ALA GLU LYS ARG ILE LYS VAL GLU LYS PRO VAL VAL SEQRES 2 B 422 GLU MET ASP GLY ASP GLU MET THR ARG ILE ILE TRP GLN SEQRES 3 B 422 PHE ILE LYS GLU LYS LEU ILE LEU PRO HIS VAL ASP VAL SEQRES 4 B 422 GLN LEU LYS TYR PHE ASP LEU GLY LEU PRO ASN ARG ASP SEQRES 5 B 422 GLN THR ASN ASP GLN VAL THR ILE ASP SER ALA LEU ALA SEQRES 6 B 422 THR GLN LYS TYR SER VAL ALA VAL LYS CYS ALA THR ILE SEQRES 7 B 422 THR PRO ASP GLU ALA ARG VAL GLU GLU PHE LYS LEU LYS SEQRES 8 B 422 LYS MET TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE SEQRES 9 B 422 LEU GLY GLY THR VAL PHE ARG GLU PRO ILE ILE CYS LYS SEQRES 10 B 422 ASN ILE PRO ARG LEU VAL PRO GLY TRP THR LYS PRO ILE SEQRES 11 B 422 THR ILE GLY ARG HIS ALA HIS GLY ASP GLN TYR LYS ALA SEQRES 12 B 422 THR ASP PHE VAL VAL ASP ARG ALA GLY THR PHE LYS LEU SEQRES 13 B 422 VAL PHE THR PRO LYS ASP GLY SER SER ALA LYS GLU TRP SEQRES 14 B 422 GLU VAL TYR ASN PHE PRO ALA GLY GLY VAL GLY MET GLY SEQRES 15 B 422 MET TYR ASN THR ASP GLU SER ILE SER GLY PHE ALA HIS SEQRES 16 B 422 SER CYS PHE GLN TYR SER ILE GLN LYS LYS TRP PRO LEU SEQRES 17 B 422 TYR LEU SER THR LYS ASN THR ILE LEU GLN ALA TYR ASP SEQRES 18 B 422 GLY ARG PHE LYS ASP ILE PHE GLN GLU ILE PHE ASP LYS SEQRES 19 B 422 HIS TYR LYS THR ASP PHE ASP LYS ASN LYS ILE TRP TYR SEQRES 20 B 422 GLU HIS ARG LEU ILE ASP ASP MET VAL ALA GLN VAL LEU SEQRES 21 B 422 LYS SER SER GLY GLY PHE VAL TRP ALA CYS LYS ASN TYR SEQRES 22 B 422 ASP GLY ASP VAL GLN SER ASP ILE LEU ALA GLN GLY PHE SEQRES 23 B 422 GLY SER LEU GLY LEU MET THR SER VAL LEU VAL CYS PRO SEQRES 24 B 422 ASP GLY LYS THR ILE GLU ALA GLU ALA ALA HIS GLY THR SEQRES 25 B 422 VAL THR ARG HIS TYR ARG GLU HIS GLN LYS GLY ARG PRO SEQRES 26 B 422 THR SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR SEQRES 27 B 422 ARG GLY LEU GLU HIS ARG GLY LYS LEU ASP GLY ASN GLN SEQRES 28 B 422 ASP LEU ILE ARG PHE ALA GLN THR LEU GLU LYS VAL CYS SEQRES 29 B 422 VAL GLN THR VAL GLU SER GLY ALA MET THR LYS ASP LEU SEQRES 30 B 422 ALA GLY CYS ILE HIS GLY LEU SER ASN VAL LYS LEU ASN SEQRES 31 B 422 GLU HIS PHE LEU ASN THR THR ASP PHE LEU ASP THR ILE SEQRES 32 B 422 LYS SER ASN LEU ASP ARG ALA LEU GLY LYS GLN LEU GLU SEQRES 33 B 422 HIS HIS HIS HIS HIS HIS HET MG A 501 1 HET ICT A 502 13 HET MG B 501 1 HET ICT B 502 13 HETNAM MG MAGNESIUM ION HETNAM ICT ISOCITRIC ACID FORMUL 3 MG 2(MG 2+) FORMUL 4 ICT 2(C6 H8 O7) FORMUL 7 HOH *128(H2 O) HELIX 1 AA1 ASP A 56 LEU A 70 1 15 HELIX 2 AA2 GLY A 85 THR A 92 1 8 HELIX 3 AA3 ASP A 94 SER A 108 1 15 HELIX 4 AA4 ASP A 119 LYS A 127 1 9 HELIX 5 AA5 SER A 134 GLY A 144 1 11 HELIX 6 AA6 GLY A 176 ALA A 181 5 6 HELIX 7 AA7 ASP A 225 LYS A 243 1 19 HELIX 8 AA8 ALA A 257 TYR A 274 1 18 HELIX 9 AA9 TYR A 274 ASN A 281 1 8 HELIX 10 AB1 ILE A 290 SER A 300 1 11 HELIX 11 AB2 LYS A 309 GLY A 325 1 17 HELIX 12 AB3 VAL A 351 LYS A 360 1 10 HELIX 13 AB4 PRO A 368 GLY A 387 1 20 HELIX 14 AB5 ASN A 388 SER A 408 1 21 HELIX 15 AB6 THR A 412 GLY A 421 1 10 HELIX 16 AB7 LEU A 422 VAL A 425 5 4 HELIX 17 AB8 ASN A 433 GLY A 450 1 18 HELIX 18 AB9 ASP B 56 LEU B 70 1 15 HELIX 19 AC1 GLY B 85 THR B 92 1 8 HELIX 20 AC2 ASP B 94 SER B 108 1 15 HELIX 21 AC3 ASP B 119 LYS B 127 1 9 HELIX 22 AC4 SER B 134 GLY B 144 1 11 HELIX 23 AC5 GLY B 176 ALA B 181 5 6 HELIX 24 AC6 ASP B 225 LYS B 243 1 19 HELIX 25 AC7 ALA B 257 TYR B 274 1 18 HELIX 26 AC8 TYR B 274 ASN B 281 1 8 HELIX 27 AC9 ILE B 290 SER B 300 1 11 HELIX 28 AD1 LYS B 309 GLY B 325 1 17 HELIX 29 AD2 VAL B 351 LYS B 360 1 10 HELIX 30 AD3 PRO B 368 GLY B 387 1 20 HELIX 31 AD4 ASN B 388 SER B 408 1 21 HELIX 32 AD5 THR B 412 GLY B 421 1 10 HELIX 33 AD6 ASN B 433 LYS B 451 1 19 SHEET 1 AA1 2 ILE A 44 LYS A 45 0 SHEET 2 AA1 2 VAL A 75 ASP A 76 1 O ASP A 76 N ILE A 44 SHEET 1 AA210 LEU A 79 ASP A 83 0 SHEET 2 AA210 VAL A 50 ASP A 54 1 N VAL A 50 O LYS A 80 SHEET 3 AA210 VAL A 109 LYS A 112 1 O VAL A 109 N VAL A 51 SHEET 4 AA210 ILE A 342 GLU A 345 1 O ALA A 344 N LYS A 112 SHEET 5 AA210 MET A 330 VAL A 335 -1 N LEU A 334 O GLU A 343 SHEET 6 AA210 THR A 146 PRO A 151 -1 N THR A 146 O VAL A 335 SHEET 7 AA210 THR A 169 HIS A 173 -1 O ARG A 172 N VAL A 147 SHEET 8 AA210 VAL A 305 CYS A 308 1 O CYS A 308 N GLY A 171 SHEET 9 AA210 LEU A 246 THR A 250 1 N TYR A 247 O ALA A 307 SHEET 10 AA210 TYR A 285 LEU A 289 1 O ARG A 288 N LEU A 248 SHEET 1 AA3 4 THR A 182 VAL A 186 0 SHEET 2 AA3 4 GLY A 216 THR A 224 -1 O GLY A 220 N THR A 182 SHEET 3 AA3 4 GLY B 216 THR B 224 -1 O VAL B 217 N ASN A 223 SHEET 4 AA3 4 THR B 182 VAL B 186 -1 N THR B 182 O GLY B 220 SHEET 1 AA4 4 LYS A 205 PHE A 212 0 SHEET 2 AA4 4 GLY A 190 PRO A 198 -1 N PHE A 192 O TYR A 210 SHEET 3 AA4 4 GLY B 190 PRO B 198 -1 O LYS B 193 N VAL A 195 SHEET 4 AA4 4 LYS B 205 PHE B 212 -1 O PHE B 212 N GLY B 190 SHEET 1 AA510 VAL B 75 ASP B 83 0 SHEET 2 AA510 ILE B 44 ASP B 54 1 N GLU B 52 O LYS B 80 SHEET 3 AA510 VAL B 109 LYS B 112 1 O VAL B 111 N MET B 53 SHEET 4 AA510 ILE B 342 GLU B 345 1 O ALA B 344 N LYS B 112 SHEET 5 AA510 MET B 330 VAL B 335 -1 N LEU B 334 O GLU B 343 SHEET 6 AA510 THR B 146 PRO B 151 -1 N THR B 146 O VAL B 335 SHEET 7 AA510 ILE B 168 HIS B 173 -1 O ARG B 172 N VAL B 147 SHEET 8 AA510 PHE B 304 CYS B 308 1 O CYS B 308 N GLY B 171 SHEET 9 AA510 LEU B 246 THR B 250 1 N TYR B 247 O ALA B 307 SHEET 10 AA510 TYR B 285 LEU B 289 1 O ARG B 288 N LEU B 248 LINK OD2 ASP A 291 MG MG B 501 1555 1555 2.23 LINK OD1 ASP A 314 MG MG A 501 1555 1555 2.15 LINK MG MG A 501 O2 ICT A 502 1555 1555 2.31 LINK MG MG A 501 O7 ICT A 502 1555 1555 2.38 LINK MG MG A 501 OD2 ASP B 291 1555 1555 2.32 LINK OD1 ASP B 314 MG MG B 501 1555 1555 2.20 LINK MG MG B 501 O7 ICT B 502 1555 1555 2.77 LINK MG MG B 501 O1 ICT B 502 1555 1555 2.25 SITE 1 AC1 4 ASP A 314 ASP A 318 ICT A 502 ASP B 291 SITE 1 AC2 13 THR A 117 SER A 134 ASN A 136 ARG A 140 SITE 2 AC2 13 ARG A 149 ARG A 172 TYR A 179 ASP A 314 SITE 3 AC2 13 MG A 501 HOH A 644 LYS B 251 ILE B 254 SITE 4 AC2 13 ASP B 291 SITE 1 AC3 4 ASP A 291 ASP B 314 ASP B 318 ICT B 502 SITE 1 AC4 13 LYS A 251 ILE A 254 ASP A 291 THR B 117 SITE 2 AC4 13 SER B 134 ASN B 136 ARG B 140 ARG B 149 SITE 3 AC4 13 ARG B 172 TYR B 179 ASP B 314 ALA B 347 SITE 4 AC4 13 MG B 501 CRYST1 58.150 58.150 206.915 90.00 90.00 120.00 P 32 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 0.017197 0.009929 0.000000 0.00000 SCALE2 0.000000 0.019857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004833 0.00000