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 METHANOSARCINA
 
Authors :  C. Kisker, H. Schindelin, D. C. Rees
Date :  02 Apr 96  (Deposition) - 14 Oct 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Carbonic Anhydrase, Lyase (Oxo-Acid) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Kisker, H. Schindelin, B. E. Alber, J. G. Ferry, D. C. Rees
A Left-Hand Beta-Helix Revealed By The Crystal Structure Of A Carbonic Anhydrase From The Archaeon Methanosarcina Thermophila.
Embo J. V. 15 2323 1996
PubMed-ID: 8665839
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBONIC ANHYDRASE
    Chains: A, B, C
    EC Number: 4.2.1.1
    Engineered: YES
    Organism Scientific: METHANOSARCINA THERMOPHILA
    Organism Taxid: 2210
    Other Details: MET 0 IS DUE TO CLONING ARTIFACT
    Synonym: CAM

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): ABC
Biological Unit 2 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ZN3Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
11UNKNOWNHIS A:81 , HIS A:122 , ZN A:214 , HOH C:215 , HIS C:117ACTIVE SITE 1, LOCATED BETWEEN A AND C CHAIN.
22UNKNOWNHIS B:81 , HIS B:122 , ZN B:214 , HOH A:215 , HIS A:117ACTIVE SITE 2, LOCATED BETWEEN B AND A CHAIN.
33UNKNOWNHIS C:81 , HIS C:122 , ZN C:214 , HOH B:215 , HIS B:117ACTIVE SITE 3, LOCATED BETWEEN C AND B CHAIN.
4AC1SOFTWAREHIS A:81 , HIS A:122 , HIS C:117 , HOH C:215BINDING SITE FOR RESIDUE ZN A 214
5AC2SOFTWAREHIS A:117 , HOH A:215 , HIS B:81 , HIS B:122BINDING SITE FOR RESIDUE ZN B 214
6AC3SOFTWAREHIS B:117 , HOH B:215 , HIS C:81 , HIS C:122BINDING SITE FOR RESIDUE ZN C 214

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1THJ)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Met A:64 -Pro A:65
2Gly A:123 -Pro A:124
3Met B:64 -Pro B:65
4Gly B:123 -Pro B:124
5Met C:64 -Pro C:65
6Gly C:123 -Pro C:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1THJ)

(-) 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 CAH_METTE | P40881 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:213
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            CAH_METTE    34 AQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPQASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKET 246
               SCOP domains d1thja_ A: gamma-carbonic anhydrase                                                                                                                                                                                   SCOP domains
               CATH domains 1thjA00 A:0-212 Hexapeptide repeat proteins                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................eeee.eee..........eeee.....eee..........eee............hhh.eee..eee.eee..........eee..eee..........eee.eee..........eee..................hhhhhh........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1thj A   0 MQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPEASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKET 212
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with CAH_METTE | P40881 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:213
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            CAH_METTE    34 AQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPQASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKET 246
               SCOP domains d1thjb_ B: gamma-carbonic anhydrase                                                                                                                                                                                   SCOP domains
               CATH domains 1thjB00 B:0-212 Hexapeptide repeat proteins                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................eeee.eee..........eeee.....eee..........eee............hhh.eee..eee.eee..........eee..eee..........eee.eee..........eee..................hhhhhh........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1thj B   0 MQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPEASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKET 212
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209   


Chain C from PDB  Type:PROTEIN  Length:213
 aligned with CAH_METTE | P40881 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:213
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
            CAH_METTE    34 AQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPQASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKET 246
               SCOP domains d1thjc_ C: gamma-carbonic anhydrase                                                                                                                                                                                   SCOP domains
               CATH domains 1thjC00 C:0-212 Hexapeptide repeat proteins                                                                                                                                                                           CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------Hexapep-1thjC01 C:106-141           ----------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------Hexapep-1thjC02 C:106-141           ----------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------Hexapep-1thjC03 C:106-141           ----------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------Hexapep-1thjC04 C:106-141           ----------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------Hexapep-1thjC05 C:106-141           ----------------------------------------------------------------------- Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------Hexapep-1thjC06 C:106-141           ----------------------------------------------------------------------- Pfam domains (6)
         Sec.struct. author .......................................eeee.eee..........eeee.....eee..........eee............hhh.eee..eee.eee..........eee..eee..........eee.eee..........eee..................hhhhhh........hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1thj C   0 MQEITVDEFSNIRENPVTPWNPEPSAPVIDPTAYIDPEASVIGEVTIGANVMVSPMASIRSDEGMPIFVGDRSNVQDGVVLHALETINEEGEPIEDNIVEVDGKEYAVYIGNNVSLAHQSQVHGPAAVGDDTFIGMQAFVFKSKVGNNCVLEPRSAAIGVTIPDGRYIPAGMVVTSQAEADKLPEVTDDYAYSHTNEAVVYVNVHLAEGYKET 212
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209
   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, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: Hexapep] (52)
(-)
Family: Hexapep (52)
(-)
Methanosarcina thermophila (6)
1aHexapep-1thjC01C:106-141
1bHexapep-1thjC02C:106-141
1cHexapep-1thjC03C:106-141
1dHexapep-1thjC04C:106-141
1eHexapep-1thjC05C:106-141
1fHexapep-1thjC06C:106-141

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (CAH_METTE | P40881)
molecular function
    GO:0004089    carbonate dehydratase activity    Catalysis of the reaction: H2CO3 = CO2 + H2O.
    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
    1  [ RasMol ]  +environment [ RasMol ]
    2  [ RasMol ]  +environment [ RasMol ]
    3  [ RasMol ]  +environment [ RasMol ]
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:123 - Pro A:124   [ RasMol ]  
    Gly B:123 - Pro B:124   [ RasMol ]  
    Gly C:123 - Pro C:124   [ RasMol ]  
    Met A:64 - Pro A:65   [ RasMol ]  
    Met B:64 - Pro B:65   [ RasMol ]  
    Met C:64 - Pro C:65   [ RasMol ]  
 
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
  1thj
    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
  CAH_METTE | P40881
    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)
  (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
  CAH_METTE | P40881
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CAH_METTE | P40881: 1qq0 1qre 1qrf 1qrg 1qrl 1qrm 3otm 3otz 3ou9 3oup 3ow5

(-) Related Entries Specified in the PDB File

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