10 20 30 40 50 60 70 80 1CW4 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXIDOREDUCTASE 25-AUG-99 1CW4
TITLE CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH TITLE 2 ALPHA-KETOGLUTARATE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.42; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PTK513; SOURCE 7 OTHER_DETAILS: VARIANT OF E. COLI STRAIN JLK1 WITH NO WILD- TYPE SOURCE 8 ISOCITRATE DEHYDROGENASE GENE
KEYWDS OXIDOREDUCTASE, ISOCITRATE DEHYDROGENASE, MUTANT
EXPDTA X-RAY DIFFRACTION
AUTHOR M.R.STROUD,J.FINER-MOORE
REVDAT 4 13-JUL-11 1CW4 1 VERSN REVDAT 3 24-FEB-09 1CW4 1 VERSN REVDAT 2 07-FEB-00 1CW4 1 JRNL SEQADV REVDAT 1 01-SEP-99 1CW4 0
JRNL AUTH D.B.CHERBAVAZ,M.E.LEE,R.M.STROUD,D.E.KOSHLAND JR. JRNL TITL ACTIVE SITE WATER MOLECULES REVEALED IN THE 2.1 A RESOLUTION JRNL TITL 2 STRUCTURE OF A SITE-DIRECTED MUTANT OF ISOCITRATE JRNL TITL 3 DEHYDROGENASE. JRNL REF J.MOL.BIOL. V. 295 377 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10623532 JRNL DOI 10.1006/JMBI.1999.3195
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.E.LEE,D.H.DYER,O.D.KLEIN,B.L.STODDARD,D.E.KOSHLAND JR. REMARK 1 TITL MUTATIONAL ANALYSIS OF THE CATALYTIC RESIDUES LYSINE 230 AND REMARK 1 TITL 2 TYROSINE 160 IN THE NADP+ DEPENDENT ISOCITRATE DEHYDROGENASE REMARK 1 TITL 3 FROM ESCHERICHIA COLI REMARK 1 REF BIOCHEMISTRY V. 34 378 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.H.HURLEY,A.M.DEAN,D.E.KOSHLAND JR.,R.M.STROUD REMARK 1 TITL CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE REMARK 1 TITL 2 DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF REMARK 1 TITL 3 MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES REMARK 1 REF BIOCHEMISTRY V. 30 8671 1991 REMARK 1 REFN ISSN 0006-2960
REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 3080652.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 38798 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 SET) : 0.184 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3899 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.22 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5779 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 678 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.009 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3174 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 334 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.31000 REMARK 3 B22 (A**2) : 1.31000 REMARK 3 B33 (A**2) : -2.61000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.30 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM11.WAT REMARK 3 PARAMETER FILE 3 : PARAM.AKG REMARK 3 PARAMETER FILE 4 : PARAM.SO4 REMARK 3 PARAMETER FILE 5 : PARAM19.ION REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPO.AKG REMARK 3 TOPOLOGY FILE 3 : TOPO.SO4 REMARK 3 TOPOLOGY FILE 4 : TOPH11.WAT REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1CW4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-99. REMARK 100 THE RCSB ID CODE IS RCSB009581.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.08 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40761 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, DTT, NAN3, MN-ALPHA- REMARK 280 KETOGLUTARATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 75.05000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.40000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.57500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.52500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.40000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.57500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.40000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.40000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.52500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.05000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER CONSTRUCTED FROM CHAIN A REMARK 300 BY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (Y,X,-Z)
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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 1
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 GLU A 2 CG CD OE1 OE2 REMARK 470 GLN A 10 CG CD OE1 NE2 REMARK 470 GLN A 17 CG CD OE1 NE2 REMARK 470 ASN A 18 CG OD1 REMARK 470 LYS A 20 CG CD CE NZ REMARK 470 ASP A 81 CG OD1 OD2 REMARK 470 LYS A 267 CG CD CE NZ REMARK 470 LYS A 344 CG CD CE NZ
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 GLN A 80 -68.03 -27.18 REMARK 500 ARG A 96 -35.93 66.44 REMARK 500 SER A 113 119.86 -31.39 REMARK 500 ASP A 148 81.19 -155.03 REMARK 500 GLU A 157 -154.83 -128.33 REMARK 500 ASP A 158 176.36 72.07 REMARK 500 ASP A 259 -125.40 57.53 REMARK 500 ARG A 292 55.84 -141.14 REMARK 500 ASP A 297 -94.94 -140.69 REMARK 500 ALA A 342 58.91 31.14 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 574 DISTANCE = 5.03 ANGSTROMS REMARK 525 HOH A 627 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 688 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 728 DISTANCE = 5.19 ANGSTROMS
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 MN A 418 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 307 OD2 REMARK 620 2 AKG A 417 O2 71.9 REMARK 620 3 AKG A 417 O5 104.4 64.6 REMARK 620 4 HOH A 490 O 63.1 64.8 129.2 REMARK 620 5 HOH A 738 O 128.3 90.2 110.8 65.3 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 417
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ICD RELATED DB: PDB REMARK 900 WILD-TYPE IDH COMPLEXES WITH MG-ISOCITRATE, ROOM REMARK 900 TEMPERATURE STRUCTURE REMARK 900 RELATED ID: 1IDC RELATED DB: PDB REMARK 900 K230M ISOCITRATE DEHYDROGENASE COMPLEXED WITH MG- REMARK 900 OXALOSUCCINATE, ROOM TEMPERATURE STRUCTURE REMARK 900 RELATED ID: 1IDF RELATED DB: PDB REMARK 900 K230M ISOCITRATE DEHYDROGENASE, ROOM TEMPERATURE APOPROTEIN REMARK 900 STRUCTURE REMARK 900 RELATED ID: 1IDD RELATED DB: PDB REMARK 900 Y160F ISOCITRATE DEHYDROGENASE, ROOM TEMPERATURE APOPROTEIN REMARK 900 STRUCTURE
DBREF 1CW4 A 1 416 UNP P08200 IDH_ECOLI 1 416
SEQADV 1CW4 MET A 230 UNP P08200 LYS 230 CONFLICT
SEQRES 1 A 416 MET GLU SER LYS VAL VAL VAL PRO ALA GLN GLY LYS LYS SEQRES 2 A 416 ILE THR LEU GLN ASN GLY LYS LEU ASN VAL PRO GLU ASN SEQRES 3 A 416 PRO ILE ILE PRO TYR ILE GLU GLY ASP GLY ILE GLY VAL SEQRES 4 A 416 ASP VAL THR PRO ALA MET LEU LYS VAL VAL ASP ALA ALA SEQRES 5 A 416 VAL GLU LYS ALA TYR LYS GLY GLU ARG LYS ILE SER TRP SEQRES 6 A 416 MET GLU ILE TYR THR GLY GLU LYS SER THR GLN VAL TYR SEQRES 7 A 416 GLY GLN ASP VAL TRP LEU PRO ALA GLU THR LEU ASP LEU SEQRES 8 A 416 ILE ARG GLU TYR ARG VAL ALA ILE LYS GLY PRO LEU THR SEQRES 9 A 416 THR PRO VAL GLY GLY GLY ILE ARG SER LEU ASN VAL ALA SEQRES 10 A 416 LEU ARG GLN GLU LEU ASP LEU TYR ILE CYS LEU ARG PRO SEQRES 11 A 416 VAL ARG TYR TYR GLN GLY THR PRO SER PRO VAL LYS HIS SEQRES 12 A 416 PRO GLU LEU THR ASP MET VAL ILE PHE ARG GLU ASN SER SEQRES 13 A 416 GLU ASP ILE TYR ALA GLY ILE GLU TRP LYS ALA ASP SER SEQRES 14 A 416 ALA ASP ALA GLU LYS VAL ILE LYS PHE LEU ARG GLU GLU SEQRES 15 A 416 MET GLY VAL LYS LYS ILE ARG PHE PRO GLU HIS CYS GLY SEQRES 16 A 416 ILE GLY ILE LYS PRO CYS SER GLU GLU GLY THR LYS ARG SEQRES 17 A 416 LEU VAL ARG ALA ALA ILE GLU TYR ALA ILE ALA ASN ASP SEQRES 18 A 416 ARG ASP SER VAL THR LEU VAL HIS MET GLY ASN ILE MET SEQRES 19 A 416 LYS PHE THR GLU GLY ALA PHE LYS ASP TRP GLY TYR GLN SEQRES 20 A 416 LEU ALA ARG GLU GLU PHE GLY GLY GLU LEU ILE ASP GLY SEQRES 21 A 416 GLY PRO TRP LEU LYS VAL LYS ASN PRO ASN THR GLY LYS SEQRES 22 A 416 GLU ILE VAL ILE LYS ASP VAL ILE ALA ASP ALA PHE LEU SEQRES 23 A 416 GLN GLN ILE LEU LEU ARG PRO ALA GLU TYR ASP VAL ILE SEQRES 24 A 416 ALA CYS MET ASN LEU ASN GLY ASP TYR ILE SER ASP ALA SEQRES 25 A 416 LEU ALA ALA GLN VAL GLY GLY ILE GLY ILE ALA PRO GLY SEQRES 26 A 416 ALA ASN ILE GLY ASP GLU CYS ALA LEU PHE GLU ALA THR SEQRES 27 A 416 HIS GLY THR ALA PRO LYS TYR ALA GLY GLN ASP LYS VAL SEQRES 28 A 416 ASN PRO GLY SER ILE ILE LEU SER ALA GLU MET MET LEU SEQRES 29 A 416 ARG HIS MET GLY TRP THR GLU ALA ALA ASP LEU ILE VAL SEQRES 30 A 416 LYS GLY MET GLU GLY ALA ILE ASN ALA LYS THR VAL THR SEQRES 31 A 416 TYR ASP PHE GLU ARG LEU MET ASP GLY ALA LYS LEU LEU SEQRES 32 A 416 LYS CYS SER GLU PHE GLY ASP ALA ILE ILE GLU ASN MET
HET MN A 418 1 HET SO4 A 419 5 HET AKG A 417 10
HETNAM MN MANGANESE (II) ION HETNAM SO4 SULFATE ION HETNAM AKG 2-OXOGLUTARIC ACID
FORMUL 2 MN MN 2+ FORMUL 3 SO4 O4 S 2- FORMUL 4 AKG C5 H6 O5 FORMUL 5 HOH *334(H2 O)
HELIX 1 1 ILE A 37 LYS A 58 1 22 HELIX 2 2 GLY A 71 GLY A 79 1 9 HELIX 3 3 PRO A 85 ARG A 96 1 12 HELIX 4 4 SER A 113 LEU A 122 1 10 HELIX 5 5 HIS A 143 LEU A 146 5 4 HELIX 6 6 ASP A 158 GLY A 162 5 5 HELIX 7 7 SER A 169 GLU A 182 1 14 HELIX 8 8 SER A 202 ASN A 220 1 19 HELIX 9 9 THR A 237 GLY A 255 1 19 HELIX 10 10 ALA A 282 ARG A 292 1 11 HELIX 11 11 PRO A 293 TYR A 296 5 4 HELIX 12 12 MET A 302 VAL A 317 1 16 HELIX 13 13 ALA A 342 ALA A 346 5 5 HELIX 14 14 PRO A 353 MET A 367 1 15 HELIX 15 15 TRP A 369 ALA A 386 1 18 HELIX 16 16 THR A 390 ARG A 395 1 6 HELIX 17 17 LYS A 404 ASN A 415 1 12
SHEET 1 A 2 THR A 15 GLN A 17 0 SHEET 2 A 2 LYS A 20 ASN A 22 -1 O LYS A 20 N GLN A 17 SHEET 1 B12 SER A 64 GLU A 67 0 SHEET 2 B12 ILE A 29 ILE A 32 1 O ILE A 29 N MET A 66 SHEET 3 B12 VAL A 97 LYS A 100 1 O ILE A 99 N ILE A 32 SHEET 4 B12 ALA A 333 GLU A 336 1 O ALA A 333 N ALA A 98 SHEET 5 B12 ALA A 326 ILE A 328 -1 O ASN A 327 N LEU A 334 SHEET 6 B12 ILE A 126 ARG A 132 -1 O ILE A 126 N ILE A 328 SHEET 7 B12 ASP A 148 GLU A 154 -1 O MET A 149 N VAL A 131 SHEET 8 B12 VAL A 298 CYS A 301 1 O ILE A 299 N PHE A 152 SHEET 9 B12 SER A 224 HIS A 229 1 O SER A 224 N VAL A 298 SHEET 10 B12 GLU A 274 ILE A 281 1 O VAL A 276 N VAL A 225 SHEET 11 B12 LEU A 264 LYS A 267 -1 O LEU A 264 N ILE A 277 SHEET 12 B12 GLU A 256 LEU A 257 -1 N GLU A 256 O LYS A 265 SHEET 1 C 2 GLU A 164 TRP A 165 0 SHEET 2 C 2 ILE A 196 GLY A 197 -1 O ILE A 196 N TRP A 165 SHEET 1 D 2 THR A 388 VAL A 389 0 SHEET 2 D 2 LYS A 401 LEU A 403 1 O LYS A 401 N VAL A 389
LINK MN MN A 418 OD2 ASP A 307 1555 1555 2.75 LINK MN MN A 418 O2 AKG A 417 1555 1555 2.53 LINK MN MN A 418 O5 AKG A 417 1555 1555 2.41 LINK MN MN A 418 O HOH A 490 1555 1555 2.67 LINK MN MN A 418 O HOH A 738 1555 1555 2.43
CISPEP 1 GLY A 261 PRO A 262 0 0.14
SITE 1 AC1 6 ASP A 283 ASP A 307 ASP A 311 AKG A 417 SITE 2 AC1 6 HOH A 490 HOH A 738 SITE 1 AC2 7 VAL A 107 GLY A 108 GLY A 109 GLY A 110 SITE 2 AC2 7 LYS A 235 HOH A 629 HOH A 650 SITE 1 AC3 12 SER A 113 ASN A 115 ARG A 119 ARG A 129 SITE 2 AC3 12 ARG A 153 TYR A 160 ILE A 233 ASP A 307 SITE 3 AC3 12 MN A 418 HOH A 482 HOH A 490 HOH A 750
CRYST1 102.800 102.800 150.100 90.00 90.00 90.00 P 43 21 2 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 0.009728 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009728 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006662 0.00000