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 :  STRUCTURE OF A SELENOMETHIONINE DERIVATIVE OF THE GH76 ALPHA-MANNANASE BT2949 BACTEROIDES THETAIOTAOMICRON
 
Authors :  A. J. Thompson, F. Cuskin, R. J. Spears, J. Dabin, J. P. Turkenburg, H. J. G. J. Davies
Date :  02 Oct 14  (Deposition) - 11 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Glycoside Hydrolase, Gh76, Cazy, Bacteroides, Polysaccharide Utilisation, Enzyme-Carbohydrate Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Thompson, F. Cuskin, R. J. Spears, J. Dabin, J. P. Turkenburg, H. J. Gilbert, G. J. Davies
Structure Of The Gh76 Alpha-Mannanase Homolog, Bt2949, From The Gut Symbiont Bacteroides Thetaiotaomicron
Acta Crystallogr. , Sect. D V. 71 408 2015
PubMed-ID: 25664752  |  Reference-DOI: 10.1107/S1399004714026443

(-) Compounds

Molecule 1 - ALPHA-1,6-MANNANASE
    Atcc: 29148
    Chains: A, B
    EC Number: 3.2.1.101
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON
    Organism Taxid: 226186
    Strain: VPI-5482

 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  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE18Mod. Amino AcidSELENOMSEHIONINE
3SRT3Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE9Mod. Amino AcidSELENOMSEHIONINE
3SRT2Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2MSE9Mod. Amino AcidSELENOMSEHIONINE
3SRT1Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:98 , LYS A:99 , SER A:100 , HOH A:2142 , HOH A:2149BINDING SITE FOR RESIDUE SRT A 400
2AC2SOFTWAREARG A:351 , ASP A:352 , GLY A:353 , GLY A:355 , HOH A:2487 , HOH A:2490 , HOH A:2491 , HOH A:2530BINDING SITE FOR RESIDUE SRT A 401
3AC3SOFTWAREASN A:232 , VAL A:236 , LYS A:285 , TYR A:286 , HOH A:2435BINDING SITE FOR RESIDUE EDO A1397
4AC4SOFTWAREASP A:60 , SER B:296 , HOH B:2404 , HOH B:2407BINDING SITE FOR RESIDUE EDO A1398
5AC5SOFTWARELYS A:99 , GLN A:160 , SER B:98 , LYS B:99 , SER B:100 , HOH B:2139BINDING SITE FOR RESIDUE SRT B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V1R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4V1R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V1R)

(-) Exons   (0, 0)

(no "Exon" information available for 4V1R)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.............eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v1r A  36 DPGVEIGNNDYYTWCKETLSVIDKDLKISGTHSYYENQDRSQVSFIWGNIFLLYTYTEGISLSKSEWSDALmNCFLNFDNYWHPNYKGIAGYATLPTSAEKVPDRFYDENGWTAIGLCDAYLATQNNSYLEKAKGALAFSLSGEDNVLGGGIYFQETFVSLPVQKNTICSAVTmLSCmKLYEITQDRQYLDAAIRINDWTVENLLDKSDNLLWDAKmVADGSVNTQKWSYNAGFmIRSWLKmYQATKDEKYLSQAKATLASSEAKWYNSINGALNDPGYFAFSIIDSWFDmYDTDKNTVWLTKAFHAINFIHNKLRDGNGRYPEHWGTPTTSNLEKYDLRFSTVAAYmYmRAANYKRILND 396
                                    45        55        65        75        85        95       105 |     115       125       135       145       155       165       175       185       195       205   |   215       225       235       245      |255       265    |  275 |     285       295       305       315       325|      335       345       355       365       375       385       395 
                                                                                                 107-MSE                                                                                               209-MSE                                    252-MSE           270-MSE  |                                              326-MSE                                                  383-MSE         
                                                                                                                                                                                                           213-MSE                                                         277-MSE                                                                                                     385-MSE       


Chain B from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.............eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eee.....ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v1r B  36 DPGVEIGNNDYYTWCKETLSVIDKDLKISGTHSYYENQDRSQVSFIWGNIFLLYTYTEGISLSKSEWSDALmNCFLNFDNYWHPNYKGIAGYATLPTSAEKVPDRFYDENGWTAIGLCDAYLATQNNSYLEKAKGALAFSLSGEDNVLGGGIYFQETFVSLPVQKNTICSAVTmLSCmKLYEITQDRQYLDAAIRINDWTVENLLDKSDNLLWDAKmVADGSVNTQKWSYNAGFmIRSWLKmYQATKDEKYLSQAKATLASSEAKWYNSINGALNDPGYFAFSIIDSWFDmYDTDKNTVWLTKAFHAINFIHNKLRDGNGRYPEHWGTPTTSNLEKYDLRFSTVAAYmYmRAANYKRILND 396
                                    45        55        65        75        85        95       105 |     115       125       135       145       155       165       175       185       195       205   |   215       225       235       245      |255       265    |  275 |     285       295       305       315       325|      335       345       355       365       375       385       395 
                                                                                                 107-MSE                                                                                               209-MSE                                    252-MSE           270-MSE  |                                              326-MSE                                                  383-MSE         
                                                                                                                                                                                                           213-MSE                                                         277-MSE                                                                                                     385-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 4V1R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V1R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V1R)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SRT  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4v1r)
 
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
  4v1r
    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
  Q8A3K5_BACTN | Q8A3K5
    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)
  3.2.1.101
    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
  Q8A3K5_BACTN | Q8A3K5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8A3K5_BACTN | Q8A3K5: 4v1s

(-) Related Entries Specified in the PDB File

4v1s STRUCTURE OF THE GH76 ALPHA-MANNANASE BT2949 FROM BACTEROIDES THETAIOTAOMICRON
4v27 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA- 1,3-ISOFAGOMINE
4v28 STRUCTURE OF AN E333Q VARIANT OF THE GH99 ENDO-ALPHA -MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MAN-MAN-METHYLUMBELLIFERONE