Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ISOCITRATE DEHYDROGENASE FROM SINORHIZOBIUM MELILOTI 1021
 
Authors :  D. Kumaran, S. Chamala, B. Evans, R. Foti, A. Gizzi, B. Hillerich, A. Kar J. Lafleur, R. Seidel, G. Villigas, W. Zencheck, S. C. Almo, S. Swamina York Structural Genomics Research Consortium (Nysgrc)
Date :  23 Nov 11  (Deposition) - 14 Dec 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Psi-Biology, Structural Genomics, Protein Structure Initiative, New York Structural Genomics Research Consortium, Nysgrc, Isocitrate Dehydrogenase, Rossmann Fold, Isocitrate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kumaran, S. C. Almo, S. Swaminathan
Crystal Structure Of An Isocitrate Dehydrogenase From Sinorhizobium Meliloti 1021
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP]
    Chains: A, B
    EC Number: 1.1.1.42
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ICD, R01792, SMC00480
    Organism Common: ENSIFER MELILOTI
    Organism Scientific: SINORHIZOBIUM MELILOTI
    Organism Taxid: 266834
    Strain: 1021

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:77 , SER A:94 , ASN A:96 , HOH A:474 , HOH A:564BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREASN A:101 , ARG A:140 , HOH A:425 , HOH A:530 , HOH A:556BINDING SITE FOR RESIDUE SO4 A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3US8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3US8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3US8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3US8)

(-) Exons   (0, 0)

(no "Exon" information available for 3US8)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:401
 aligned with Q92PG6_RHIME | Q92PG6 from UniProtKB/TrEMBL  Length:404

    Alignment length:401
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401 
         Q92PG6_RHIME     2 AKIKVANPVVELDGDEMTRIIWQFIKDKLIHPYLDLDLEYYDLGVENRDATDDQVTIDAANAIKKHGVGVKCATITPDEGRVEEFKLKKMWKSPNGTIRNILGGVIFREPIICKNVPRLVPGWTKPIIVGRHAFGDQYRATDFKFPGKGKLSIKFVGEDGQTIEHDVYDAPGAGVALAMYNLDESITEFARASFNYGLQRKVPVYLSTKNTILKAYDGRFKDIFQKVFDEEFAAQFKAEKLWYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDGKTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNAELAKFSETLERVCVDTVESGFMTKDLALLIGPDQPWLSTTGFLDKIDENLRKAM 402
               SCOP domains d3us8a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee....eeeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3us8 A   2 AKIKVANPVVELDGDEmTRIIWQFIKDKLIHPYLDLDLEYYDLGVENRDATDDQVTIDAANAIKKHGVGVKCATITPDEGRVEEFKLKKmWKSPNGTIRNILGGVIFREPIICKNVPRLVPGWTKPIIVGRHAFGDQYRATDFKFPGKGKLSIKFVGEDGQTIEHDVYDAPGAGVALAmYNLDESITEFARASFNYGLQRKVPVYLSTKNTILKAYDGRFKDIFQKVFDEEFAAQFKAEKLWYEHRLIDDmVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLmTSVLmTPDGKTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNAELAKFSETLERVCVDTVESGFmTKDLALLIGPDQPWLSTTGFLDKIDENLRKAm 402
                                    11      | 21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251|      261       271       281       291  |    301       311       321       331       341       351       361       371       381       391       401|
                                           18-MSE                                                                   91-MSE                                                                                  180-MSE                                                                 252-MSE                              289-MSE|                                                                         370-MSE                         402-MSE
                                                                                                                                                                                                                                                                                                                              294-MSE                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:401
 aligned with Q92PG6_RHIME | Q92PG6 from UniProtKB/TrEMBL  Length:404

    Alignment length:401
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402 
         Q92PG6_RHIME     3 KIKVANPVVELDGDEMTRIIWQFIKDKLIHPYLDLDLEYYDLGVENRDATDDQVTIDAANAIKKHGVGVKCATITPDEGRVEEFKLKKMWKSPNGTIRNILGGVIFREPIICKNVPRLVPGWTKPIIVGRHAFGDQYRATDFKFPGKGKLSIKFVGEDGQTIEHDVYDAPGAGVALAMYNLDESITEFARASFNYGLQRKVPVYLSTKNTILKAYDGRFKDIFQKVFDEEFAAQFKAEKLWYEHRLIDDMVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLMTSVLMTPDGKTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNAELAKFSETLERVCVDTVESGFMTKDLALLIGPDQPWLSTTGFLDKIDENLRKAMA 403
               SCOP domains d3us8b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee................eeeeee..hhhhhheeeee...eeeeeeeee....eeeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3us8 B   3 KIKVANPVVELDGDEmTRIIWQFIKDKLIHPYLDLDLEYYDLGVENRDATDDQVTIDAANAIKKHGVGVKCATITPDEGRVEEFKLKKmWKSPNGTIRNILGGVIFREPIICKNVPRLVPGWTKPIIVGRHAFGDQYRATDFKFPGKGKLSIKFVGEDGQTIEHDVYDAPGAGVALAmYNLDESITEFARASFNYGLQRKVPVYLSTKNTILKAYDGRFKDIFQKVFDEEFAAQFKAEKLWYEHRLIDDmVASALKWSGGYVWACKNYDGDVQSDIVAQGFGSLGLmTSVLmTPDGKTVEAEAAHGTVTRHYRQHQKGEETSTNSIASIFAWTRGLAHRAKLDGNAELAKFSETLERVCVDTVESGFmTKDLALLIGPDQPWLSTTGFLDKIDENLRKAmA 403
                                    12     |  22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      |292 |     302       312       322       332       342       352       362       372       382       392       402 
                                          18-MSE                                                                   91-MSE                                                                                  180-MSE                                                                 252-MSE                              289-MSE|                                                                         370-MSE                         402-MSE
                                                                                                                                                                                                                                                                                                                             294-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3US8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3US8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q92PG6_RHIME | Q92PG6)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004450    isocitrate dehydrogenase (NADP+) activity    Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0006102    isocitrate metabolic process    The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate cycle.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3us8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3us8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q92PG6_RHIME | Q92PG6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.42
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q92PG6_RHIME | Q92PG6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3US8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3US8)