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 THE HUMAN CARBONIC ANHYDRASE RELATED PROTEIN VIII
 
Authors :  A. Kramm, J. R. C. Muniz, S. S. Picaud, F. Von Delft, E. S. Pilka, W. W. Yue O. N. F. King, G. Kochan, A. C. W. Pike, P. Filippakopoulos, C. Arrowsmith, M. Wikstrom, A. Edwards, C. Bountra, U. Oppermann
Date :  31 Oct 08  (Deposition) - 03 Feb 09  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Lyase, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Picaud, J. R. C. Muniz, A. Kramm, E. S. Pilka, G. Kochan, U. Oppermann, W. W. Yue
Crystal Structure Of Human Carbonic Anhydrase- Related Protein Viii Reveals The Basis For Catalytic Silencing.
Proteins V. 76 507 2009
PubMed-ID: 19360879  |  Reference-DOI: 10.1002/PROT.22411

(-) Compounds

Molecule 1 - CARBONIC ANHYDRASE-RELATED PROTEIN
    Chains: A
    EC Number: 4.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC28-BSA4
    Expression System Strain: BL21(DE3)-R3-PRARE2
    Expression System Taxid: 469008
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CARP, CARBONIC ANHYDRASE VIII, CA-VIII, CA8A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3UNX3Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:116 , HIS A:118 , HIS A:141BINDING SITE FOR RESIDUE CL A 401
02AC2SOFTWAREGLU A:32BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREARG A:252BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWAREGLU A:24 , SER A:56 , TRP A:216 , ARG A:237 , HOH A:2157 , HOH A:2322BINDING SITE FOR RESIDUE GOL A 501
05AC5SOFTWAREARG A:125 , GLY A:126 , SER A:127 , ALA A:135 , PHE A:274 , HOH A:2323 , HOH A:2324 , HOH A:2325 , HOH A:2326 , HOH A:2327 , HOH A:2328BINDING SITE FOR RESIDUE GOL A 502
06AC6SOFTWAREVAL A:98 , GLU A:109 , GLU A:111 , PRO A:279 , HOH A:2164 , HOH A:2329 , HOH A:2330 , HOH A:2331BINDING SITE FOR RESIDUE GOL A 503
07AC7SOFTWAREGLY A:173 , LYS A:174 , HOH A:2332BINDING SITE FOR RESIDUE GOL A 504
08AC8SOFTWARELEU A:149 , HOH A:2158 , HOH A:2159 , HOH A:2169 , HOH A:2333 , HOH A:2334 , HOH A:2335BINDING SITE FOR RESIDUE GOL A 505
09AC9SOFTWARESER A:56 , ALA A:59 , ALA A:287 , PHE A:289 , GLN A:290 , HOH A:2049 , HOH A:2336BINDING SITE FOR RESIDUE GOL A 506
10BC1SOFTWAREASP A:154 , UNX A:602 , UNX A:603BINDING SITE FOR RESIDUE UNX A 601
11BC2SOFTWAREUNX A:601BINDING SITE FOR RESIDUE UNX A 602
12BC3SOFTWAREUNX A:601BINDING SITE FOR RESIDUE UNX A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W2J)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:50 -Pro A:51
2Pro A:225 -Pro A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063634S100PCAH8_HUMANDisease (CMARQ3)267606695AS100P
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_CA_2PS51144 Alpha-carbonic anhydrases profile.CAH8_HUMAN27-289  1A:27-289
2ALPHA_CA_1PS00162 Alpha-carbonic anhydrases signature.CAH8_HUMAN127-143  1A:127-143

(-) Exons   (0, 0)

(no "Exon" information available for 2W2J)

(-) 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:268
 aligned with CAH8_HUMAN | P35219 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:268
                                    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        
           CAH8_HUMAN    23 EEEGVEWGYEEGVEWGLVFPDANGEYQSPINLNSREARYDPSLLDVRLSPNYVVCRDCEVTNDGHTIQVILKSKSVLSGGPLPQGHEFELYEVRFHWGRENQRGSEHTVNFKAFPMELHLIHWNSTLFGSIDEAVGKPHGIAIIALFVQIGKEHVGLKAVTEILQDIQYKGKSKTIPCFNPNTLLPDPLLRDYWVYEGSLTIPPCSEGVTWILFRYPLTISQLQIEEFRRLRTHVKGAELVEGCDGILGDNFRPTQPLSDRVIRAAFQ 290
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2w2jA00 A:23-290 Carbonic Anhydrase II                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------Carb_anhydrase-2w2jA01 A:29-289                                                                                                                                                                                                                                      - Pfam domains
         Sec.struct. author .............hhhhhhhhhhh......eehhhhhee.hhhhh..........................................eeeeeeeeee..........ee......eeeeeeeee.....hhhhhh.....eeeeeeeeee...hhhhhhhhhhhhhhh...........hhhhhh.......eeeeeee.......eeeeeeee......hhhhhhhhh..................................ee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------P---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----ALPHA_CA_2  PDB: A:27-289 UniProt: 27-289                                                                                                                                                                                                                              - PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------ALPHA_CA_1       --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2j A  23 EEEGVEWGYEEGVEWGLVFPDANGEYQSPINLNSREARYDPSLLDVRLSPNYVVCRDCEVTNDGHTIQVILKSKSVLSGGPLPQGHEFELYEVRFHWGRENQRGSEHTVNFKAFPMELHLIHWNSTLFGSIDEAVGKPHGIAIIALFVQIGKEHVGLKAVTEILQDIQYKGKSKTIPCFNPNTLLPDPLLRDYWVYEGSLTIPPCSEGVTWILFRYPLTISQLQIEEFRRLRTHVKGAELVEGCDGILGDNFRPTQPLSDRVIRAAFQ 290
                                    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
   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 2W2J)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Carb_anhydrase] (168)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CAH8_HUMAN | P35219)
molecular function
    GO:0004089    carbonate dehydratase activity    Catalysis of the reaction: H2CO3 = CO2 + H2O.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNX  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:225 - Pro A:226   [ RasMol ]  
    Ser A:50 - Pro A:51   [ RasMol ]  
 

(-) 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
  2w2j
    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
  CAH8_HUMAN | P35219
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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)
  613227
    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
  CAH8_HUMAN | P35219
    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 2W2J)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W2J)