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
(-)Biological Unit 3
(-)Biological Unit 4
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF CHITINASE FROM RALSTONIA SP. A-471 IN COMPLEX WITH DISACCHARIDE
 
Authors :  T. Arimori, N. Kawamoto, N. Okazaki, M. Nakazawa, K. Miyatake, T. Fukam M. Ueda, T. Tamada
Date :  14 Feb 13  (Deposition) - 15 May 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Gh Family 23, Enzyme, Glycoside Hydrolase, Chitinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Arimori, N. Kawamoto, S. Shinya, N. Okazaki, M. Nakazawa, K. Miyatake, T. Fukamizo, M. Ueda, T. Tamada
Crystal Structures Of The Catalytic Domain Of A Novel Glycohydrolase Family 23 Chitinase From Ralstonia Sp. A-471 Reveals A Unique Arrangement Of The Catalytic Residues For Inverting Chitin Hydrolysis
J. Biol. Chem. V. 288 18696 2013
PubMed-ID: 23658014  |  Reference-DOI: 10.1074/JBC.M113.462135

(-) Compounds

Molecule 1 - LYSOZYME-LIKE CHITINOLYTIC ENZYME
    Chains: A, B, C, D
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD I
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN, UNP RESIDUES 89-252
    Organism Scientific: RALSTONIA
    Organism Taxid: 200912
    Strain: A-471

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:160 , VAL A:161 , GLU A:162 , THR A:165 , ALA A:168 , TYR A:214 , ASN A:215 , GLY A:217 , ASP A:218 , TYR A:219 , HOH A:418 , HOH A:423BINDING SITE FOR LINKED RESIDUES A 301 to 302
2AC2SOFTWARELYS A:140 , GLU A:141 , SER A:142 , TYR A:143 , GLY A:147 , SER A:151 , SER A:153 , GLN A:160 , ASN A:215 , ARG A:230 , TYR A:237 , HOH A:438BINDING SITE FOR LINKED RESIDUES A 303 to 304
3AC3SOFTWAREVAL B:161 , GLU B:162 , THR B:165 , TYR B:214 , ASN B:215 , GLY B:217 , ASP B:218 , TYR B:219 , TRP B:220 , ASP B:226 , SER B:227 , HOH B:401 , HOH B:458 , HOH B:468BINDING SITE FOR LINKED RESIDUES B 301 to 302
4AC4SOFTWAREVAL A:103 , MET A:118 , LYS B:140 , GLU B:141 , SER B:142 , TYR B:143 , GLY B:147 , SER B:151 , SER B:153 , GLN B:160 , ASN B:215 , ARG B:230 , TYR B:237 , HOH B:463BINDING SITE FOR LINKED RESIDUES B 303 to 304
5AC5SOFTWAREVAL C:161 , GLU C:162 , THR C:165 , TYR C:214 , ASN C:215 , GLY C:216 , GLY C:217 , ASP C:218 , TYR C:219 , HOH C:436 , HOH C:440BINDING SITE FOR LINKED RESIDUES C 301 to 302
6AC6SOFTWAREVAL D:161 , GLU D:162 , ASN D:164 , THR D:165 , ALA D:168 , TYR D:214 , ASN D:215 , GLY D:217 , ASP D:218 , TYR D:219 , SER D:227 , HOH D:410 , HOH D:429 , HOH D:432BINDING SITE FOR LINKED RESIDUES D 301 to 302
7AC7SOFTWARELYS D:140 , GLU D:141 , SER D:142 , GLY D:147 , SER D:151 , SER D:153 , GLN D:160 , ASN D:215 , ARG D:230 , TYR D:237 , HOH D:433 , HOH D:454 , HOH D:471BINDING SITE FOR LINKED RESIDUES D 303 to 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W6C)

(-) Exons   (0, 0)

(no "Exon" information available for 3W6C)

(-) 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:151
 aligned with B7XCV4_9RALS | B7XCV4 from UniProtKB/TrEMBL  Length:252

    Alignment length:151
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
         B7XCV4_9RALS   102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRY 252
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w6c A 102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRY 252
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with B7XCV4_9RALS | B7XCV4 from UniProtKB/TrEMBL  Length:252

    Alignment length:153
                                                                                                                                                                                252  
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251|  
         B7XCV4_9RALS   102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRY--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w6c B 102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRYSR 254
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   


Chain C from PDB  Type:PROTEIN  Length:153
 aligned with B7XCV4_9RALS | B7XCV4 from UniProtKB/TrEMBL  Length:252

    Alignment length:153
                                                                                                                                                                                252  
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251|  
         B7XCV4_9RALS   102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRY--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w6c C 102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRYSR 254
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251   


Chain D from PDB  Type:PROTEIN  Length:153
 aligned with B7XCV4_9RALS | B7XCV4 from UniProtKB/TrEMBL  Length:252

    Alignment length:153
                                                                                                                                                                                252  
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251|  
         B7XCV4_9RALS   102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRY--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w6c D 102 TVTKPAEVPSRIWTYVMNADNAYGKGGDFALLLSAVIKKESYFGDGLSGSPSAGDGLMQVEPNTRNAYLSQFSAKYGHAYNHSSEQDQVYMGSLILNEKIVRFGSIYSGLLHYNGGDYWYPGATDSYGRPILADQYANTVYAQYKSYGGRYSR 254
                                   111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 3W6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W6C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W6C)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (B7XCV4_9RALS | B7XCV4)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

 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
    NAG  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3w6c)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 3 PNG format | Biol. Unit 4 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
  3w6c
    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
  B7XCV4_9RALS | B7XCV4
    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
  B7XCV4_9RALS | B7XCV4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        B7XCV4_9RALS | B7XCV4: 3w6b 3w6d 3w6e 3w6f

(-) Related Entries Specified in the PDB File

3w6b 3w6d 3w6e 3w6f