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 :  STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF A CHITIN-ACTIVE 15.5 KDA LYTIC POLYSACCHARIDE MONOOXYGENASE DOMAIN FROM A MODULAR CHITINASE FROM JONESIA DENITRIFICANS
 
Authors :  S. Mekasha, Z. Forsberg, B. Dalhus, S. Choudhary, C. Schmidt-Dannert, G. Vaaje-Kolstad, V. Eijsink
Date :  23 Jul 15  (Deposition) - 09 Dec 15  (Release) - 06 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mekasha, Z. Forsberg, B. Dalhus, J. Bacik, S. Choudhary, C. Schmidt-Dannert, G. Vaaje-Kolstad, V. G. H. Eijsink
Structural And Functional Characterization Of A Small Chitin-Active Lytic Polysaccharide Monooxygenase Domain Of A Multi-Modular Chitinase From Jonesia Denitrificans.
Febs Lett. V. 590 34 2016
PubMed-ID: 26763108  |  Reference-DOI: 10.1002/1873-3468.12025

(-) Compounds

Molecule 1 - CHITINASE
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: 15.5 KDA LYTIC POLYSACCHARIDE MONOOXYGENASE, RESIDUES 32-17 DOMAIN
    Organism Scientific: JONESIA DENITRIFICANS
    Organism Taxid: 43674
    Synonym: 3LPMOA

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CU12Ligand/IonCOPPER (I) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CU11Ligand/IonCOPPER (I) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:32 , HIS A:109 , PHE A:164BINDING SITE FOR RESIDUE CU1 A1143
2AC2SOFTWAREHIS B:32 , HIS B:109 , PHE B:164BINDING SITE FOR RESIDUE CU1 B1143

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:45 -A:54
2A:73 -A:167
3B:45 -B:54
4B:73 -B:167

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:37 -Pro A:38
2Asp B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AA7)

(-) Exons   (0, 0)

(no "Exon" information available for 5AA7)

(-) 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:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhh......hhhhhhhhhh.eee.........hhhhhhhhh.......eee...eeeeeee.....eeeeeeee..eeeeeee........eeeeee.....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aa7 A  32 HGWVTDPPSRQALCASGETSFDCGQISYEPQSVEAPKGATTCSGGNEAFAILDDNSKPWPTTEIASTVDLTWKLTAPHNTSTWEYFVDGQLHQTFDQKGQQPPTSLTHTLTDLPTGEHTILARWNVSNTNNAFYNCMDVVVS 173
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171  


Chain B from PDB  Type:PROTEIN  Length:142
                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhh......hhhhhhhhhh.eee.........hhhhhhhhh.......eee...eeeeeee.....eeeeeeee..eeeeeee........eeeeee.....eeeeeeeeeee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aa7 B  32 HGWVTDPPSRQALCASGETSFDCGQISYEPQSVEAPKGATTCSGGNEAFAILDDNSKPWPTTEIASTVDLTWKLTAPHNTSTWEYFVDGQLHQTFDQKGQQPPTSLTHTLTDLPTGEHTILARWNVSNTNNAFYNCMDVVVS 173
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171
   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 5AA7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AA7)

(-) Gene Ontology  (9, 9)

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
    CU1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asp A:37 - Pro A:38   [ RasMol ]  
    Asp B:37 - Pro B:38   [ 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
  5aa7
    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
  C7R4I0_JONDD | C7R4I0
    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)
  3.2.1.14
    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
  C7R4I0_JONDD | C7R4I0
    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
        C7R4I0_JONDD | C7R4I0: 5vg0 5vg1

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5AA7)