Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CARBONIC ANHYDRASE FROM MARINE DIATOM THALASSIOSIRA WEISSFLOGII-CADMIUM BOUND DOMAIN 1 WITH ACETATE (CDCA1-R1)
 
Authors :  Y. Xu, L. Feng, P. D. Jeffrey, Y. Shi, F. M. M. Morel
Date :  17 Dec 07  (Deposition) - 22 Jan 08  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Carbonic Anhydrase, Marine Diatom, Cadmium-Bound, Acetate Bound, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xu, L. Feng, P. D. Jeffrey, Y. Shi, F. M. Morel
Structure And Metal Exchange In The Cadmium Carbonic Anhydrase Of Marine Diatoms.
Nature V. 452 56 2008
PubMed-ID: 18322527  |  Reference-DOI: 10.1038/NATURE06636

(-) Compounds

Molecule 1 - CADMIUM-SPECIFIC CARBONIC ANHYDRASE
    Chains: A, B
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAIN 1, CDCA1-R1
    Gene: CDCA1
    Organism Scientific: THALASSIOSIRA WEISSFLOGII
    Organism Taxid: 67004

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD2Ligand/IonCADMIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CD-1Ligand/IonCADMIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:53 , HIS A:105 , CYS A:115 , ACT A:1002 , HOH A:1003BINDING SITE FOR RESIDUE CD A 1001
2AC2SOFTWARECYS A:53 , VAL A:54 , GLY A:116 , PHE A:117 , HIS A:159 , THR A:207 , LEU A:211 , CD A:1001 , HOH A:1003 , HOH A:1083BINDING SITE FOR RESIDUE ACT A 1002
3AC3SOFTWARECYS B:53 , HIS B:105 , CYS B:115 , ACT B:1002 , HOH B:1004BINDING SITE FOR RESIDUE CD B 1001
4AC4SOFTWARECYS B:53 , VAL B:54 , GLY B:116 , PHE B:117 , THR B:207 , LEU B:211 , CD B:1001 , HOH B:1004BINDING SITE FOR RESIDUE ACT B 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BOH)

(-) 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:213
 aligned with Q50EL4_THAWE | Q50EL4 from UniProtKB/TrEMBL  Length:616

    Alignment length:213
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403   
         Q50EL4_THAWE   194 VIPSISPAQIAEALQGRGWDAEIVTDASMAGQLVDVRPEGILKCVDGRGSDNTRMGGPKMPGGIYAIAHNRGVTSIEGLKQITKEVASKGHLPSVHGDHSSDMLGCGFFKLWVTGRFDDMGYPRPQFDADQGANAVKDAGGIIEMHHGSHTEKVVYINLLANKTLEPNENDQRFIVDGWAADKFGLDVPKFLIAAAATVEMLGGPKNAKIVVP 406
               SCOP domains -----------------d3boha1 A:27-222 Cadmium-specific carbonic anhydrase CdCA1                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeeeee.hhhh...ee.....ee.....................hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhh..eeeee........eeee....ee.........eeeehhhhhhh..hhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3boh A  10 SHMSLTPDQIVAALQERGWQAEIVTEFSLLNEMVDVDPQGILKCVDGRGSDNTQFCGPKMPGGIYAIAHNRGVTTLEGLKQITKEVASKGHVPSVHGDHSSDMLGCGFFKLWVTGRFDDMGYPRPQFDADQGAKAVENAGGVIEMHHGSHAEKVVYINLVENKTLEPDEDDQRFIVDGWAAGKFGLDVPKFLIAAAATVEMLGGPKKAKIVIP 222
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q50EL4_THAWE | Q50EL4 from UniProtKB/TrEMBL  Length:616

    Alignment length:213
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403   
         Q50EL4_THAWE   194 VIPSISPAQIAEALQGRGWDAEIVTDASMAGQLVDVRPEGILKCVDGRGSDNTRMGGPKMPGGIYAIAHNRGVTSIEGLKQITKEVASKGHLPSVHGDHSSDMLGCGFFKLWVTGRFDDMGYPRPQFDADQGANAVKDAGGIIEMHHGSHTEKVVYINLLANKTLEPNENDQRFIVDGWAADKFGLDVPKFLIAAAATVEMLGGPKNAKIVVP 406
               SCOP domains d3bohb_ B: Cadmium-specific carbonic anhydrase CdCA1                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh..eeeeee.hhhhhhhee.....ee.....................hhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhh..eeeee........eeee....ee.........eeeehhhhhhh..hhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3boh B  10 SHMSLTPDQIVAALQERGWQAEIVTEFSLLNEMVDVDPQGILKCVDGRGSDNTQFCGPKMPGGIYAIAHNRGVTTLEGLKQITKEVASKGHVPSVHGDHSSDMLGCGFFKLWVTGRFDDMGYPRPQFDADQGAKAVENAGGVIEMHHGSHAEKVVYINLVENKTLEPDEDDQRFIVDGWAAGKFGLDVPKFLIAAAATVEMLGGPKKAKIVIP 222
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q50EL4_THAWE | Q50EL4)
molecular function
    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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3boh)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  3boh
    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
  Q50EL4_THAWE | Q50EL4
    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)
  4.2.1.1
    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
  Q50EL4_THAWE | Q50EL4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q50EL4_THAWE | Q50EL4: 3bob 3boc 3boe 3boj 3uk8

(-) Related Entries Specified in the PDB File

3bob CDCA1-R2 WITH CADMIUM
3boc CDCA1-R2 WITH ZINC
3boe CDCA1-R2 WITH CADMIUM AND ACETATE