Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
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 GH18 CHITINASE FROM CYCAD, CYCAS REVOLUTA
 
Authors :  N. Umemoto, T. Numata, T. Ohnuma, T. Osawa, T. Taira, T. Fukamizo
Date :  11 Sep 13  (Deposition) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Chitinase, Hydrolase, Carbohydrate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Umemoto, T. Numata, T. Ohnuma, T. Osawa, T. Taira, T. Fukamizo
Crystal Structure Of Gh18 Chitinase From Cycad, Cycas Revoluta
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CHITINASE A
    Chains: A
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 24-370
    Gene: CRCHIA
    Organism Common: SAGO PALM
    Organism Scientific: CYCAS REVOLUTA
    Organism Taxid: 3396

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:130 , VAL A:131 , VAL A:134 , GLU A:157 , ILE A:179BINDING SITE FOR RESIDUE ACT A 401
2AC2SOFTWAREGLN A:177 , HOH A:548 , HOH A:560BINDING SITE FOR RESIDUE ACT A 402
3AC3SOFTWAREPHE A:8 , ASP A:115 , ASP A:117 , ALA A:158 , ASN A:187 , HOH A:656BINDING SITE FOR RESIDUE ACT A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ala A:33 -Phe A:34
2Ala A:39 -Pro A:40
3Glu A:119 -Tyr A:120
4Glu A:122 -Pro A:123
5Leu A:165 -Phe A:166
6Pro A:263 -Val A:264
7Trp A:327 -Ser A:328

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MNJ)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhh...hhhhhhhhhh.eeeeeee..............hhhhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...ee......ee.hhhhhhhhh.eeeee.......................hhhhhhhhhhhhh.hhh.eeeeee.eeeeeee...........eeee.....eeehhhhhhhhhh..eeeee....eeeeee..eeeee.hhhhhhhhhhhhhhh...eeeee.hhhh..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mnj A   3 ALKVGFWPAYSVSEFPPSKINSRLFTHLYYAFAELNAPTFEVRVPPGSEKTAEDFTPTVRRLNPSVKTLISIGGGGSEVRDNFAKLNSDASARQRFVKSSIALARRYGFHGLDLDYEYPEPQLEMENFVKLVSELTAAIREEARTSGKPRLLLTEAVYFHQKLFPWEVVTEYPVQFIAAGLDWVNVMAYDFHGSWENFTGAPAALRDSKFTASVGIESFLAAGMPPEKLVLGIPLFGRSWLLKNNNEVGIGAPAVGAGPVDGALSFSEIQNFIRGGAREVFDTTTVSAYAYKDNVWVGYDNQQSVALKVQYAKEKRLGGYFFWSVNQDIDAILPKIASDTWG 346
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202      |214       224       234       244       254       264       274       284       294       304       314       324       334       344  
                                                                                                                                                                                                                                        209|                                                                                                                                      
                                                                                                                                                                                                                                         212
   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 4MNJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:33 - Phe A:34   [ RasMol ]  
    Ala A:39 - Pro A:40   [ RasMol ]  
    Glu A:119 - Tyr A:120   [ RasMol ]  
    Glu A:122 - Pro A:123   [ RasMol ]  
    Leu A:165 - Phe A:166   [ RasMol ]  
    Pro A:263 - Val A:264   [ RasMol ]  
    Trp A:327 - Ser A:328   [ 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
  4mnj
    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
  Q4W6L6_CYCRE | Q4W6L6
    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
  Q4W6L6_CYCRE | Q4W6L6
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q4W6L6_CYCRE | Q4W6L6: 3wij 4mnk 4mnl 4mnm 4r5e

(-) Related Entries Specified in the PDB File

4mnk 4mnl 4mnm