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 :  CRYSTAL STRUCTURE OF XEG5A, A GH5 XYLOGLUCAN-SPECIFIC ENDO-BETA-1,4-GLUCANASE FROM RUMINAL METAGENOMIC LIBRARY, IN COMPLEX WITH GLUCOSE
 
Authors :  C. R. Santos, R. L. Cordeiro, D. W. S. Wong, M. T. Murakami
Date :  22 Aug 14  (Deposition) - 11 Mar 15  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoside Hydrolase, Cell Wall Degrading Enzyme, Gh5 Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. R. Dos Santos, R. L. Cordeiro, D. W. Wong, M. T. Murakami
Structural Basis For Xyloglucan Specificity And Alpha-D-Xylp(1 6)-D-Glcp Recognition At The -1 Subsite Within The Gh5 Family.
Biochemistry V. 54 1930 2015
PubMed-ID: 25714929  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00011

(-) Compounds

Molecule 1 - XYLOGLUCAN-SPECIFIC ENDO-BETA-1,4-GLUCANASE
    Chains: A, B
    EC Number: 3.2.1.151
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: UNCULTURED BACTERIUM
    Organism Taxid: 77133

 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
1BGC2Ligand/IonBETA-D-GLUCOSE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:111 , ASN A:184 , ASP A:185 , GLY A:186binding site for residue BGC A 501
2AC2SOFTWAREHOH A:721 , HOH A:722 , HOH A:723 , HOH A:724 , HOH B:732 , HOH B:733binding site for residue MG A 502
3AC3SOFTWAREASN B:111 , HOH B:740binding site for residue BGC B 501
4AC4SOFTWAREHOH A:725 , HOH A:726 , HOH B:734 , HOH B:735 , HOH B:736 , HOH B:737binding site for residue MG B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W85)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:162 -Pro A:163
2Thr A:317 -Pro A:318
3Ala B:162 -Pro B:163
4Thr B:317 -Pro B:318

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W85)

(-) Exons   (0, 0)

(no "Exon" information available for 4W85)

(-) 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:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...eeee...........hhhhhhh......hhhhhhhhhhhh..eeee...hhhhh........hhhhhhhhhhhhhhhhhh..eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh.hhhhhhh........eeeeee...hhhhhh............hhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......................hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w85 A  92 DRSRVFDILSNINIGWNLGNTLDATGGGNSVNAETSWGNPKTTQEIVDTVNDRGFNAIRIPVTFANHLGPAPEYTISADWLARVKEVVDYAVNDGMYIILDTHHETNYWLKTDPNNEAALCEELAAIWKQLAEAFKDYDEKLMFEGMNEPRMAGSAKEWSGGTPAERKLINAMNKAFIDAVRATGGNNADRVLIICTYGHNSDEPTLKDLEIPSDPNIAVALHTYTPYFFTYVADGSYSVWNGSKKNDITWQYNNIKKYLIDKGIPVVITETGAQFKENTEDIVRWIGDYVGTLDQDGVKCFIWDNNIYHGNGEKFGLLNRSLLKWYNDDIVDAYVNHA 430
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421         


Chain B from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh...eeee...........hhhhhhh......hhhhhhhhhhhh..eeee...hhhhh........hhhhhhhhhhhhhhhhhh..eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh......eeee.................hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhh.hhhhhhh........eeeeee...hhhhhh............hhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhh...eeeeee......................hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w85 B  92 DRSRVFDILSNINIGWNLGNTLDATGGGNSVNAETSWGNPKTTQEIVDTVNDRGFNAIRIPVTFANHLGPAPEYTISADWLARVKEVVDYAVNDGMYIILDTHHETNYWLKTDPNNEAALCEELAAIWKQLAEAFKDYDEKLMFEGMNEPRMAGSAKEWSGGTPAERKLINAMNKAFIDAVRATGGNNADRVLIICTYGHNSDEPTLKDLEIPSDPNIAVALHTYTPYFFTYVADGSYSVWNGSKKNDITWQYNNIKKYLIDKGIPVVITETGAQFKENTEDIVRWIGDYVGTLDQDGVKCFIWDNNIYHGNGEKFGLLNRSLLKWYNDDIVDAYVNHA 430
                                   101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421
   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 4W85)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W85)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W85)

(-) Gene Ontology  (6, 6)

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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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
    Ala A:162 - Pro A:163   [ RasMol ]  
    Ala B:162 - Pro B:163   [ RasMol ]  
    Thr A:317 - Pro A:318   [ RasMol ]  
    Thr B:317 - Pro B:318   [ 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
  4w85
    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
  D2K7Z0_9BACT | D2K7Z0
    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)
  3.2.1.151
    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
  D2K7Z0_9BACT | D2K7Z0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        D2K7Z0_9BACT | D2K7Z0: 4w84 4w86 4w87 4w88 4w89

(-) Related Entries Specified in the PDB File

4w84 4w86 4w87 4w88 4w89 4w8a 4w8b