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 CLASS I CHITINASE FROM ORYZA SATIVA L. JAPONICA
 
Authors :  Y. Kezuka, Y. Nishizawa, T. Watanabe, T. Nonaka
Date :  14 Apr 06  (Deposition) - 01 May 07  (Release) - 21 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Class I Chitinase, Whole Structure, Oryza Sativa L. Japonica, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kezuka, M. Kojima, R. Mizuno, K. Suzuki, T. Watanabe, T. Nonaka
Structure Of Full-Length Class I Chitinase From Rice Revealed By X-Ray Crystallography And Small-Angle X-Ray Scattering
Proteins 2010
PubMed: search  |  Reference-DOI: 10.1002/PROT.22742
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE
    ChainsA
    EC Number3.2.1.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B(+)
    Expression System StrainORIGAMI B(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificORYZA SATIVA JAPONICA GROUP
    Organism Taxid39947
    StrainJAPONICA
    SynonymGLYCOSIDE HYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:204 , GLN A:205 , LEU A:206 , SER A:207 , ASN A:211 , PHE A:244 , VAL A:285 , ASN A:286 , HOH A:471BINDING SITE FOR RESIDUE MES A 341
2AC2SOFTWAREPRO A:45 , ASN A:46 , PRO A:179 , PRO A:180 , SER A:181 , ASP A:182 , PRO A:295 , ASP A:297 , HOH A:466BINDING SITE FOR RESIDUE MES A 342
3AC3SOFTWAREARG A:142 , ILE A:259BINDING SITE FOR RESIDUE MPD A 343
4AC4SOFTWAREGLY A:157 , CYS A:172 , PHE A:173 , PRO A:194BINDING SITE FOR RESIDUE MPD A 344

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:50
2A:44 -A:56
3A:47 -A:74
4A:49 -A:63
5A:67 -A:71
6A:110 -A:172
7A:184 -A:192
8A:291 -A:323

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DKV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHIT_BIND_I_1PS00026 Chitin recognition or binding domain signature.CHI2_ORYSJ44-63  1A:44-63
2CHITINASE_19_1PS00773 Chitinases family 19 signature 1.CHI2_ORYSJ110-132  1A:110-132
3CHITINASE_19_2PS00774 Chitinases family 19 signature 2.CHI2_ORYSJ236-246  1A:236-246

(-) Exons   (0, 0)

(no "Exon" information available for 2DKV)

(-) 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:286
 aligned with CHI2_ORYSJ | Q7DNA1 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:298
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322        
           CHI2_ORYSJ    33 EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQCSGCGPTPTPTPPSPSDGVGSIVPRDLFERLLLHRNDGACPARGFYTYEAFLAAAAAFPAFGGTGNTETRKREVAAFLGQTSHETTGGWPTAPDGPFSWGYCFKQEQNPPSDYCQPSPEWPCAPGRKYYGRGPIQLSFNFNYGPAGRAIGVDLLSNPDLVATDATVSFKTALWFWMTPQGNKPSSHDVITGRWAPSPADAAAGRAPGYGVITNIVNGGLECGHGPDDRVANRIGFYQRYCGAFGIGTGGNLDCYNQRPFN 330
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dkvA01 A:33-73                          2            dkvA02 A:74-174,A:233-330  [code=1.10.530.10, no name defined]                          2dkvA03 A:175-231 Endochitinase, domain 2                -2dkvA02 A:74-174,A:233-330  [code=1.10.530.10, no name defined]                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhee.....ee.hhhhhh..........------------.hhhhh.hhhhhhhhh..............hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhh........hhhhh......................................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------CHIT_BIND_I_1       ----------------------------------------------CHITINASE_19_1         -------------------------------------------------------------------------------------------------------CHITINASE_1------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dkv A  33 EQCGAQAGGARCPNCLCCSRWGWCGTTSDFCGDGCQSQCSGC------------DGVGSIVPRDLFERLLLHRNDGACPARGFYTYEAFLAAAAAFPAFGGTGNTETRKREVAAFLGQTSHETTGGWPTAPDGPFSWGYCFKQEQNPPSDYCQPSPEWPCAPGRKYYGRGPIQLSFNFNYGPAGRAIGVDLLSNPDLVATDATVSFKTALWFWMTPQGNKPSSHDVITGRWAPSPADAAAGRAPGYGVITNIVNGGLECGHGPDDRVANRIGFYQRYCGAFGIGTGGNLDCYNQRPFN 330
                                    42        52        62        72 |       -    |   92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322        
                                                                    74           87                                                                                                                                                                                                                                                   

   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 2DKV)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DKV)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHI2_ORYSJ | Q7DNA1)
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.
    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.
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: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.
    GO:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    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/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
    MES  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ 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
(no "Cis Peptide Bonds" information available for 2dkv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2dkv
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CHI2_ORYSJ | Q7DNA1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.14
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CHI2_ORYSJ | Q7DNA1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CHI2_ORYSJ | Q7DNA13iwr

(-) Related Entries Specified in the PDB File

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