2WNX - JenaLib

Title :   3B' CARBOHYDRATE-BINDING MODULE FROM THE CEL9V GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM THERMOCELLUM

Authors :   S. Petkun, S. Jindou, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow

Date :   20 Jul 09 (Deposition) - 29 Dec 09 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.31

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Cellulose Degradation, Hydrolase, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Petkun, S. Jindou, L. J. W. Shimon, E. A. Bayer, R. Lamed, F. Frolow
Structure Of A Family 3B' Carbohydrate-Binding Module From The Cel9V Glycoside Hydrolase From Clostridium Thermocellum: Structural Diversity And Implications For Carbohydrate Binding
Acta Crystallogr. , Sect. D V. 66 33 2010
PubMed-ID: 20057047 | Reference-DOI: 10.1107/S0907444909043030
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:55 , ASP A:57 , ASP A:125 , ASP A:128 , ASP A:129 , HOH A:2271	BINDING SITE FOR RESIDUE CA A1163
2	AC2	SOFTWARE	LYS A:22 , ASP A:23 , GLY A:24 , THR A:25 , LYS A:26 , ASN A:27 , THR A:28 , ARG A:30 , GLY A:58 , HOH A:2062 , HOH A:2080 , HOH A:2081	BINDING SITE FOR RESIDUE SO4 A1164
3	AC3	SOFTWARE	LYS A:36 , HOH A:2251 , HOH A:2346 , HOH A:2347	BINDING SITE FOR RESIDUE SO4 A1165
4	AC4	SOFTWARE	LYS A:77 , THR A:99 , GLU A:100 , HOH A:2234 , HOH A:2348 , HOH A:2349	BINDING SITE FOR RESIDUE SO4 A1166
5	AC5	SOFTWARE	ASN A:62 , ILE A:79 , VAL A:80 , HOH A:2183	BINDING SITE FOR RESIDUE FMT A1167

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:157
 aligned with A3DJ30_CLOTH | A3DJ30 from UniProtKB/TrEMBL  Length:961

    Alignment length:157
                                   744       754       764       774       784       794       804       814       824       834       844       854       864       874       884       
         A3DJ30_CLOTH   735 TPDANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEPVT 891
               SCOP domains d2wnxa_ A: automated matches                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------CBM_3-2wnxA01 A:15-97                                                              ----------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.eeeeeee........eeeeeeeeee.....ee...eeeeeee.......eeeee.....hhh.eeeeeeeeeeee..eeeeeeeee.....ee........eeeeeee....hhhhh...hhhhh.........eeee..eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wnx A   6 TPDANASISVSYKCGVKDGTKNTIRATINIKNTGTTPVNLSDIKVRYWFTSDGNEQNNFVCDYAAFGTDKVKGIVKKIENSVPGADTYCEISFTEDAGRLAPGGSTGTIPFRIEGAAEYDQTDDYSYNSEMSDDFGDNTKITAYIKDKLKYGVEAAA 162
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (A3DJ30_CLOTH | A3DJ30)

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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0030248	cellulose binding	Interacting selectively and non-covalently with cellulose.
	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:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	Catalysis of the hydrolysis of any O-glycosyl bond.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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: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 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wnx)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2wnx
		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
	A3DJ30_CLOTH \| A3DJ30
		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
	A3DJ30_CLOTH \| A3DJ30
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description