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
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)

(-) Description

Title :  CLOSTRIDIUM THERMOCELLUM FAMILY 3 CARBOHYDRATE ESTERASE
 
Authors :  M. A. S. Correia, J. A. M. Prates, J. Bras, C. M. G. A. Fontes, J. A. Newman, R. J. Lewis, H. J. Gilbert, J. E. Flint
Date :  04 Mar 08  (Deposition) - 06 May 08  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Esterase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. S. Correia, J. A. M. Prates, J. Bras, C. M. G. A. Fontes, J. A. Newman, R. J. Lewis, H. J. Gilbert, J. E. Flint
Crystal Structure Of A Cellulosomal Family 3 Carbohydrate Esterase From Clostridium Thermocellum Provides Insights Into The Mechanism Of Substrate Recognition
J. Mol. Biol. V. 379 64 2008
PubMed-ID: 18436237  |  Reference-DOI: 10.1016/J.JMB.2008.03.037

(-) Compounds

Molecule 1 - LIPOLYTIC ENZYME
    Atcc: 27405
    Chains: A
    EC Number: 3.1.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: CATALYTIC DOMAIN, RESIDUES 32-237
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: FAMILY 3 CARBOHYDRATE ESTERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:73 , PHE A:74 , ASP A:87 , ASP A:89 , HOH A:2082 , HOH A:2088BINDING SITE FOR RESIDUE CA A1235

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VPT)

(-) 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:201
 aligned with A3DDK4_CLOTH | A3DDK4 from UniProtKB/TrEMBL  Length:528

    Alignment length:201
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
         A3DDK4_CLOTH    34 KTIKIMPVGDSCTEGMGGGEMGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGLHLSEIGYKKIANIWYKYTIDILRALAG 234
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Lipase_GDSL-2vptA01 A:38-221                                                                                                                                                            ------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhh........hhhhhhhhhhhh..eeee...ee.........eeee....hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeehhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vpt A  34 KTIKImPVGDSCTEGmGGGEmGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGLHLSEIGYKKIANIWYKYTIDILRALAG 234
                                 |  43     |  53|       63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
                                 |        49-MSE|                                                                                                                                                                                    
                                39-MSE         54-MSE                                                                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:201
 aligned with GUNX_CLOTM | P15329 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:201
                                                                       9                                                                                                                                                             
                                1  4                        5 7       8|                   10                                                                                                                                        
                                |  | -         -         -  | |    -  ||     -         -    |   15        25        35        45        55        65        75        85        95       105       115       125       135       145 
           GUNX_CLOTM     - ----IMKV------------------------TQD-------GS--------------------IPQIASNINNWLNTHNPDVVFLWIGGNDLLLSGNVNATGLSNLIDQIFTVKPNVTLFVADYYPWPEAVKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGLHLSEIGYTKIANIWYKYTIDILKALAG 146
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Lipase_GDSL-2vptA01 A:38-221                                                                                                                                                            ------------- Pfam domains
         Sec.struct. author .eeeeeeeehhhhhh........hhhhhhhhhhhh..eeee...ee.........eeee....hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh..hhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeehhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vpt A  34 KTIKImPVGDSCTEGmGGGEmGSYRTELYRLLTQAGLSIDFVGSQRSGPSSLPDKDHEGHSGWTIPQIASNINNWLNTHNPDVVFLWIGGNDLLLNGNLNATGLSNLIDQIFTVKPNVTLFVADYYPWPEAIKQYNAVIPGIVQQKANAGKKVYFVKLSEIQFDRNTDISWDGLHLSEIGYKKIANIWYKYTIDILRALAG 234
                                 |  43     |  53|       63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
                                39-MSE    49-MSE|                                                                                                                                                                                    
                                               54-MSE
   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 2VPT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2VPT)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SGNH_hydrolase (17)

(-) Gene Ontology  (9, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (A3DDK4_CLOTH | A3DDK4)
molecular function
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

Chain A   (GUNX_CLOTM | P15329)
molecular function
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:161 - Pro A:162   [ RasMol ]  
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2vpt
    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
  A3DDK4_CLOTH | A3DDK4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  GUNX_CLOTM | P15329
    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)
  3.1.1.72
    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
  A3DDK4_CLOTH | A3DDK4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GUNX_CLOTM | P15329
    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 2VPT)

(-) Related Entries Specified in the PDB File

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