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 ARSENATE REDUCTASE FROM ARCHAEOGLOBUS FULGIDUS DSM 4304, STRUCTURAL GENOMICS
 
Authors :  Y. Patskovsky, S. C. Almo, S. K. Burley, New York Sgx Research Cente Structural Genomics (Nysgxrc)
Date :  18 Nov 04  (Deposition) - 30 Nov 04  (Release) - 15 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Arsenate Reductase, Detoxification, Cadmium, Oxidized Form, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, S. C. Almo
Crystal Structure Of Arsenate Reductase From Archaeoglobus Fulgidus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ARSENATE REDUCTASE (ARSC)
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AF1361
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1CD8Ligand/IonCADMIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:8 , GLU D:35BINDING SITE FOR RESIDUE CD A 125
2AC2SOFTWAREASP A:88 , HIS B:95BINDING SITE FOR RESIDUE CD B 125
3AC3SOFTWAREHIS B:8 , GLU C:35BINDING SITE FOR RESIDUE CD B 126
4AC4SOFTWAREHIS A:95 , ASP B:88BINDING SITE FOR RESIDUE CD B 127
5AC5SOFTWAREGLU B:35 , HIS C:8BINDING SITE FOR RESIDUE CD C 125
6AC6SOFTWAREASP C:88 , HIS D:95BINDING SITE FOR RESIDUE CD C 126
7AC7SOFTWAREGLU A:35 , HIS D:8BINDING SITE FOR RESIDUE CD D 125
8AC8SOFTWAREHIS C:95 , ASP D:88BINDING SITE FOR RESIDUE CD D 126

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:77 -A:82
2B:77 -B:82
3C:77 -C:82
4D:77 -D:82

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y1L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y1L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y1L)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y1L)

(-) 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:124
 aligned with O28910_ARCFU | O28910 from UniProtKB/TrEMBL  Length:135

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
         O28910_ARCFU     2 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 125
               SCOP domains d1y1la_ A: Arsenate reductase ArsC                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh......eeeee.......hhhhhhhhhh..........hhhhhhhhhh..eeeee.............eeeee.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y1l A   1 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain B from PDB  Type:PROTEIN  Length:124
 aligned with O28910_ARCFU | O28910 from UniProtKB/TrEMBL  Length:135

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
         O28910_ARCFU     2 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 125
               SCOP domains d1y1lb_ B: Arsenate reductase ArsC                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhh..........hhhhhhhhhh.eeeeee.............eeeee.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y1l B   1 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain C from PDB  Type:PROTEIN  Length:124
 aligned with O28910_ARCFU | O28910 from UniProtKB/TrEMBL  Length:135

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
         O28910_ARCFU     2 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 125
               SCOP domains d1y1lc_ C: Arsenate reductase ArsC                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhh..........hhhhhhhhhh..eeeee.............eeeee.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y1l C   1 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120    


Chain D from PDB  Type:PROTEIN  Length:124
 aligned with O28910_ARCFU | O28910 from UniProtKB/TrEMBL  Length:135

    Alignment length:124
                                    11        21        31        41        51        61        71        81        91       101       111       121    
         O28910_ARCFU     2 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 125
               SCOP domains d1y1ld_ D: Arsenate reductase ArsC                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -LMWPc-1y1lD01 D:2-122                                                                                                    -- Pfam domains (1)
           Pfam domains (2) -LMWPc-1y1lD02 D:2-122                                                                                                    -- Pfam domains (2)
           Pfam domains (3) -LMWPc-1y1lD03 D:2-122                                                                                                    -- Pfam domains (3)
           Pfam domains (4) -LMWPc-1y1lD04 D:2-122                                                                                                    -- Pfam domains (4)
         Sec.struct. author .eeeee....hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhh..........hhhhhhhhhh.eeeeee.............eeeee.........hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y1l D   1 KVLFVCIHNTARSVMAEALFNAMAKSWKAESAGVEKAERVDETVKRLLAERGLKAKEKPRTVDEVNLDDFDLIVTVCEESSCVVLPTDKPVTRWHIENPAGKDEGTYRRVLAEIEERVKKLVGE 124
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y1L)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: LMWPc] (24)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1Y1L)

 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
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1y1l)
 

(-) 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
  1y1l
    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
  O28910_ARCFU | O28910
    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
  O28910_ARCFU | O28910
    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 1Y1L)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1Y1L)