Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF IMP DEHYDROGENASE/GMP REDUCTASE-LIKE PROTEIN (NP_599840.1) FROM CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  27 Jul 07  (Deposition) - 14 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Np_599840. 1, Imp Dehydrogenase/Gmp Reductase-Like Protein, Gmp Reductase Domain, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Imp Dehydrogenase/Gmp Reductase-Like Protein (Np_599840. 1) From Corynebacterium Glutamicum Atcc 13032 Kitasato At 1. 50 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - IMP DEHYDROGENASE/GMP REDUCTASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_599840.1, GUAB3, CGL0604, CG0700
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM ATCC 13032
    Organism Taxid: 196627
    Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025
    Synonym: IMP DEHYDROGENASE / GMP REDUCTASE C TERMINUS, IMP DEHYDROGENASE / GMP REDUCTASE DOMAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 32)
No.NameCountTypeFull Name
1MSE32Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QR6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QR6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:198 -Gly A:199
2Gly A:336 -Pro A:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QR6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QR6)

(-) Exons   (0, 0)

(no "Exon" information available for 2QR6)

(-) Sequences/Alignments

Asymmetric 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:371
 aligned with Q8NSR4_CORGL | Q8NSR4 from UniProtKB/TrEMBL  Length:374

    Alignment length:380
                                  1                                                                                                                                                                                                                                                                                                                                                                                     
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374
         Q8NSR4_CORGL     - ------MRDHVEIGIGREARRTYSLDDISVVSSRRTRSSKDVDTTWHIDAYKFDLPFMNHPSDALASPEFVIEMGKQGGLGVINAEGLWGRHADLDEAIAKVIAAYEEGDQAAATRTLQELHAAPLDTELLSERIAQVRDSGEIVAVRVSPQNVREIAPIVIKAGADLLVIQGTLISAEHVNTGGEALNLKEFIGSLDVPVIAGGVNDYTTALHMMRTGAVGIIVGGGENTNSLALGMEVSMATAIADVAAARRDYLDETGGRYVHIIADGSIENSGDVVKAIACGADAVVLGSPLARAEEAAGKGYFWPAVAAHPRFPRGVVTESVDLDEAAPSLEQILHGPSTMPWGVENFEGGLKRALAKCGYTDLKSFQKVSLHVN 374
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qr6A01 A:-5-15      2qr6A02 A:16-374 Aldolase class I                                                                                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains --------------------IMPDH-2qr6A01 A:15-306                                                                                                                                                                                                                                                                              ---------------    ------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhheeeee..eeee...hhh.eee.......hhhhh...eee..eee...eee.......hhhhhhhhhhh....eee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhh...eeeee...........-----hhhhhhhhh...eeee...hhhhhhhhhh....eeee.....hhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhh..eeeehhhhhhh.......ee.hhhhhh........ee..----...hhhhhhhh.........hhhhhhhhhhhhhh..hhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qr6 A  -5 NLYFQGmRDHVEIGIGREARRTYSLDDISVVSSRRTRSSKDVDTTWHIDAYKFDLPFmNHPSDALASPEFVIEmGKQGGLGVINAEGLWGRHADLDEAIAKVIAAYEEGDQAAATRTLQELHAAPLDTELLSERIAQVRDSGEIVAVRVSPQNVREIAPIVIKAGADLLVIQGTLISAEHVNT-----NLKEFIGSLDVPVIAGGVNDYTTALHmmRTGAVGIIVGGGENTNSLALGmEVSmATAIADVAAARRDYLDETGGRYVHIIADGSIENSGDVVKAIACGADAVVLGSPLARAEEAAGKGYFWPAVAAHPRFPRGVVTESV----AAPSLEQILHGPSTmPWGVENFEGGLKRALAKCGYTDLKSFQKVSLHVN 374
                                  |  4        14        24        34        44       |54        64   |    74        84        94       104       114       124       134       144       154       164       174  |    184       194       204    || 214       224       234 |     244       254       264       274       284       294       304       314      |  - |     334     | 344       354       364       374
                                  1-MSE                                             52-MSE          68-MSE                                                                                                      177   183                       209-MSE                232-MSE                                                                                  321  326           340-MSE                              
                                                                                                                                                                                                                                                 210-MSE                   236-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  (0, 0)

(no "SCOP Domain" information available for 2QR6)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8NSR4_CORGL | Q8NSR4)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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.
biological process
    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.

 Visualization

(-) Interactive Views

Asymmetric 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 ]
 
  Sites
(no "Sites" information available for 2qr6)
 
  Cis Peptide Bonds
    Gly A:198 - Gly A:199   [ RasMol ]  
    Gly A:336 - Pro A:337   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  2qr6
    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
  Q8NSR4_CORGL | Q8NSR4
    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)
  (no 'Enzyme Classificator' available)
    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
  Q8NSR4_CORGL | Q8NSR4
    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 2QR6)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QR6)