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 :  CRYSTALLOGRAPHIC STRUCTURE ANALYSIS OF FAMILY 18 CHITINASE FROM CROCUS VERNUS
 
Authors :  A. Akrem, S. Iqbal, F. Buck, A. Negm, M. Perbandt, C. Betzel
Date :  19 Jun 11  (Deposition) - 06 Jul 11  (Release) - 06 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Family 18 Plant Chitinase, Tim Barrel, Chitin Binding, Glycosyl Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Akrem, S. Iqbal, F. Buck, A. Negm, M. Perbandt, C. Betzel
Crystallographic Structure Analysis Of Family 18 Chitinase From Crocus Vernus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN, FAMILY 18 CHITINASE
    Chains: A, B
    Organism Scientific: CROCUS VERNUS
    Organism Taxid: 87752

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:48 , ASN A:53 , HOH A:566 , ARG B:264BINDING SITE FOR RESIDUE ACT A 276
2AC2SOFTWAREALA A:96 , ASN A:131 , THR A:132 , ASP A:133BINDING SITE FOR RESIDUE GOL A 277
3AC3SOFTWAREGLU B:127 , GLN B:186 , ALA B:189BINDING SITE FOR RESIDUE GOL B 276

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SIM)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Tyr A:9 -Pro A:10
2Ser A:34 -Phe A:35
3Ser A:43 -Pro A:44
4Trp A:253 -Thr A:254
5Tyr B:9 -Pro B:10
6Ser B:34 -Phe B:35
7Ser B:43 -Pro B:44
8Trp B:253 -Thr B:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SIM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SIM)

(-) Exons   (0, 0)

(no "Exon" information available for 3SIM)

(-) 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:275
 aligned with G1K3S3_CROVR | G1K3S3 from UniProtKB/TrEMBL  Length:275

    Alignment length:275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
         G1K3S3_CROVR     1 TLFVEYIGYPLFSGVKFSDVPINPHITKFQFVLSFAVDYTASSPHTSTNGKFNVFWDSSILGPDQISAIKSSHPNVRVAVSLGGASVGSNTVQFQAASVDSWVSNAVTSLTRIIQRYNLDGIDIDYEHFQNTDKNTFAECIGRLITTLKKNGVISFASISPFPSVDEYYLALFNEYKNAINHINYQFKAYDSSTSVDKFLGYYNNAASKYKGGNVLISFSTGPHPGGLPVDKGFFDAATSLKNKGKLHGIAVWTADTSKSSDFRYEEEAQAFLVS 275
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........hhhhh.......eeeeeeeeee...............ee.......hhhhhhhhhhhh..eeeeeeee..ee..ee......hhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh.eee.hhhhh....hhhhhhhhhhhhhhhh....eeeeee............hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sim A   1 TLFVEYIGYPLFSGVKFSDVPINPHITKFQFVLSFAVDYTASSPHTSTNGKFNVFWDSSILGPDQISAIKSSHPNVRVAVSLGGASVGSNTVQFQAASVDSWVSNAVTSLTRIIQRYNLDGIDIDYEHFQNTDKNTFAECIGRLITTLKKNGVISFASISPFPSVDEYYLALFNEYKNAINHINYQFKAYDSSTSVDKFLGYYNNAASKYKGGNVLISFSTGPHPGGLPVDKGFFDAATSLKNKGKLHGIAVWTADTSKSSDFRYEEEAQAFLVS 275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     


Chain B from PDB  Type:PROTEIN  Length:275
 aligned with G1K3S3_CROVR | G1K3S3 from UniProtKB/TrEMBL  Length:275

    Alignment length:275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     
         G1K3S3_CROVR     1 TLFVEYIGYPLFSGVKFSDVPINPHITKFQFVLSFAVDYTASSPHTSTNGKFNVFWDSSILGPDQISAIKSSHPNVRVAVSLGGASVGSNTVQFQAASVDSWVSNAVTSLTRIIQRYNLDGIDIDYEHFQNTDKNTFAECIGRLITTLKKNGVISFASISPFPSVDEYYLALFNEYKNAINHINYQFKAYDSSTSVDKFLGYYNNAASKYKGGNVLISFSTGPHPGGLPVDKGFFDAATSLKNKGKLHGIAVWTADTSKSSDFRYEEEAQAFLVS 275
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........hhhhh.......eeeeeeeeee...............ee.......hhhhhhhhhhhh..eeeeeeee..ee..ee......hhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh.eee.hhhhh....hhhhhhhhhhhhhhhh....eeeeee............hhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sim B   1 TLFVEYIGYPLFSGVKFSDVPINPHITKFQFVLSFAVDYTASSPHTSTNGKFNVFWDSSILGPDQISAIKSSHPNVRVAVSLGGASVGSNTVQFQAASVDSWVSNAVTSLTRIIQRYNLDGIDIDYEHFQNTDKNTFAECIGRLITTLKKNGVISFASISPFPSVDEYYLALFNEYKNAINHINYQFKAYDSSTSVDKFLGYYNNAASKYKGGNVLISFSTGPHPGGLPVDKGFFDAATSLKNKGKLHGIAVWTADTSKSSDFRYEEEAQAFLVS 275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270
   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 3SIM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SIM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SIM)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (G1K3S3_CROVR | G1K3S3)
molecular function
    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.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-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: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.

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:34 - Phe A:35   [ RasMol ]  
    Ser A:43 - Pro A:44   [ RasMol ]  
    Ser B:34 - Phe B:35   [ RasMol ]  
    Ser B:43 - Pro B:44   [ RasMol ]  
    Trp A:253 - Thr A:254   [ RasMol ]  
    Trp B:253 - Thr B:254   [ RasMol ]  
    Tyr A:9 - Pro A:10   [ RasMol ]  
    Tyr B:9 - Pro B:10   [ 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
  3sim
    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
  G1K3S3_CROVR | G1K3S3
    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)
  (no 'Enzyme Classificator' available)
    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
  G1K3S3_CROVR | G1K3S3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3SIM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3SIM)