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

(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYOXALASE FROM CLOSTRIDIUM ACETOBUTYLICUM
 
Authors :  K. N. Rao, S. K. Burley, S. Swaminathan, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  29 Jun 07  (Deposition) - 17 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glyoxalase, 11003P, Clostridium Acetobutylicum, Psi-2, Nysgxrc, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. N. Rao, S. K. Burley, S. Swaminathan
Crystal Structure Of A Glyoxalase From Clostridium Acetobutylicum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTOYLGLUTATHIONE LYASE
    Atcc824
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneCA_C2192
    Organism ScientificCLOSTRIDIUM ACETOBUTYLICUM
    Organism Taxid1488
    StrainVKM B-1787, DSM 792, JCM 1419, LMG 5710

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:7 , GLU A:54 , HIS A:77 , GLU A:126 , HOH A:452BINDING SITE FOR RESIDUE ZN A 450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QH0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QH0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QH0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QH0)

(-) Exons   (0, 0)

(no "Exon" information available for 2QH0)

(-) 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:129
 aligned with Q97H22_CLOAB | Q97H22 from UniProtKB/TrEMBL  Length:128

    Alignment length:129
                             1                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119         
         Q97H22_CLOAB     - -MKVHHIGYAVKNIDSALKKFKRLGYVEESEVVRDEVRKVYIQFVINGGYRVELVAPDGEDSPINKTIKKGSTPYHICYEVEDIQKSIEEMSQIGYTLFKKAEIAPAIDNRKVAFLFSTDIGLIELLEK 128
               SCOP domains d2qh0a_ A: automated matches                                                                                                      SCOP domains
               CATH domains 2qh0A00 A:2-130 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                   CATH domains
               Pfam domains ----Glyoxalase_4-2qh0A01 A:6-116                                                                                   -------------- Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhh..ee....eee....eeeeeeee..eeeeeeee.....hhhhhh....eeeeeeeee.hhhhhhhhhhh...eeeeeeee.hhhh..eeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qh0 A   2 SLKVHHIGYAVKNIDSALKKFKRLGYVEESEVVRDEVRKVYIQFVINGGYRVELVAPDGEDSPINKTIKKGSTPYHICYEVEDIQKSIEEMSQIGYTLFKKAEIAPAIDNRKVAFLFSTDIGLIELLEK 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q97H22_CLOAB | Q97H22)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 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
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qh0)
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2qh0
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q97H22_CLOAB | Q97H22
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q97H22_CLOAB | Q97H22
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q97H22_CLOAB | Q97H223hdp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QH0)