Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CHLORIDE BOUND BRASSICA JUNCEA CHITINASE CATALYTIC MODULE (BJCHI3)
 
Authors :  W. Ubhayasekera, T. Bergfors, S. L. Mowbray
Date :  02 Jun 07  (Deposition) - 19 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Chitinase, Endochitinase, Family 19, Conformational Changes, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ubhayasekera, C. M. Tang, S. W. T. Ho, G. Berglund, T. Bergfors, M. -L. Chye, S. L. Mowbray
Crystal Structures Of A Family 19 Chitinase From Brassica Juncea Show Flexibility Of Binding Cleft Loops
Febs J. V. 274 3695 2007
PubMed-ID: 17608716  |  Reference-DOI: 10.1111/J.1742-4658.2007.05906.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE
    Chains: A
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Strain: KM71
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC MODULE, UNP RESIDUES 145-389
    Gene: BJCHI1
    Organism Scientific: BRASSICA JUNCEA
    Organism Taxid: 3707

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1CL12Ligand/IonCHLORIDE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:153 , TYR A:157 , PHE A:186 , PRO A:187 , SER A:188BINDING SITE FOR RESIDUE CL A 1001
02AC2SOFTWARELYS A:232BINDING SITE FOR RESIDUE CL A 1002
03AC3SOFTWAREPHE A:256 , ARG A:260BINDING SITE FOR RESIDUE CL A 1003
04AC4SOFTWAREASN A:164BINDING SITE FOR RESIDUE CL A 1004
05AC5SOFTWAREARG A:153 , HOH A:1073BINDING SITE FOR RESIDUE CL A 1005
06AC6SOFTWAREASN A:225 , ASN A:379 , HOH A:1150BINDING SITE FOR RESIDUE CL A 1006
07AC7SOFTWAREGLY A:219 , ALA A:224BINDING SITE FOR RESIDUE CL A 1007
08AC8SOFTWAREASN A:191 , HOH A:1200BINDING SITE FOR RESIDUE CL A 1008
09AC9SOFTWARELYS A:357 , CL A:1000 , HOH A:1099BINDING SITE FOR RESIDUE CL A 1009
10BC1SOFTWAREHIS A:211 , LYS A:357 , CL A:1009 , HOH A:1238BINDING SITE FOR RESIDUE CL A 1000
11BC2SOFTWAREGLU A:143 , ASN A:166 , HOH A:1105BINDING SITE FOR RESIDUE CL A 1010

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:168 -A:230
2A:242 -A:251
3A:350 -A:382

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:309 -Pro A:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z38)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z38)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z38)

(-) Sequences/Alignments

Asymmetric/Biological 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:247
 aligned with Q9SQF7_BRAJU | Q9SQF7 from UniProtKB/TrEMBL  Length:400

    Alignment length:247
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       
         Q9SQF7_BRAJU   143 PSGDLSGIISRDQFYKMLKHMNDNDCHAVGFFTYDAFITAAKSFPSFGNTGDLAMRKKEIAAFFGQTSHETTGGWSGAPDGANTWGYCYKEEIDKSDPHCDSNNLEWPCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFKTAIWFWMTPQAPKPSCHDVITDQWEPSAADISAGRLPGYGVITNIINGGLECAGRDVAKVQDRISFYTRYCGMFGVDPGSNIDCDNQRPFN 389
               SCOP domains d2z38a_ A: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains 2z38A01 A:143-232,A:292-389  [code=1.10.530.10, no name defined]                          2z38A02 A:233-291 Endochitinase, domain 2                  2z38A01 A:143-232,A:292-389  [code=1.10.530.10, no name defined]                                   CATH domains
               Pfam domains -------Glyco_hydro_19-2z38A01 A:150-382                                                                                                                                                                                                         ------- Pfam domains
         Sec.struct. author ...hhhhh.hhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.........hhhhh.......................................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z38 A 143 EFGDLSGIISRDQFYKMLKHMNDNDCHAVGFFTYDAFITAAKSFPSFGNTGDLAMRKKEIAAFFGQTSHETTGGWSGAPDGANTWGYCYKEEIDKSDPHCDSNNLEWPCAPGKFYYGRGPMMLSWNYNYGPCGRDLGLELLKNPDVASSDPVIAFKTAIWFWMTPQAPKPSCHDVITDQWEPSAADISAGRLPGYGVITNIINGGLECAGRDVAKVQDRISFYTRYCGMFGVDPGSNIDCDNQRPFN 389
                                   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9SQF7_BRAJU | Q9SQF7)
molecular function
    GO:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
biological process
    GO:0016998    cell wall macromolecule catabolic process    The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:309 - Pro A:310   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - 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
  2z38
    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
  Q9SQF7_BRAJU | Q9SQF7
    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
  Q9SQF7_BRAJU | Q9SQF7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9SQF7_BRAJU | Q9SQF7: 2z37 2z39

(-) Related Entries Specified in the PDB File

2z37 BRASSICA JUNCEA CATALYTIC MODULE WITHOUT CHLORIDES
2z39 BRASSICA JUNCEA CATALYTIC MODULE GLU234ALA MUTANT WITH BOUND CHLORIDE IONS