1OD3	Hydrolase	date	Feb 12, 2003
title	Structure Of Cscbm6-3 From Clostridium Stercorarium In Compl Laminaribiose
authors	A.B.Boraston, V.Notenboom, R.A.J.Warren, D.G.Kilburn, D.R.Rose, G
compound		source
Molecule: Putative Xylanase Chain: A Fragment: Carbohydrate-Binding Domain, Residues 285-417 Synonym: Endo-Xylanase, Cscbm6-3, Xyna Engineered: Yes		Organism_scientific: Clostridium Stercorarium Organism_taxid: 1510 Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_vector: Pet28 Expression_system_plasmid: Pet28-Cbm6-3
symmetry	Space Group: P 21 21 21	R_factor 0.131 R_Free 0.149
crystal cell	length a length b length c angle alpha angle beta angle gamma 36.183 52.154 64.755 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.00 Å
ligand	ACY, BGC, CA	enzyme
note	1OD3 is a representative structure
related structures	by homologous chain: 1O8S
Gene Ontology	Chain Function Process Component A
Primary reference	Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains., Boraston AB, Notenboom V, Warren RA, Kilburn DG, Rose DR, Davies G, J Mol Biol 2003 Mar 28;327(3):659-69. PMID:12634060

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk] Biological Unit Coordinates (1od3.pdb1.gz) 52 Kb LPC: Ligand-Protein Contacts for 1OD3 CSU: Contacts of Structural Units for 1OD3 Likely Quarternary Molecular Structure file(s) for 1OD3 Structure Factors (874 Kb) Retrieve 1OD3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1OD3 from S2C, [Save to disk] Re-refined 1od3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1OD3 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 1OD3

Ramachandran plot from PDBSum

Structure-derived information

Conformational Epitope Prediction for 1OD3 from the CEP Server. Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1OD3, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1od3a_, region A [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1od3] [1od3_A] SWISS-PROT database: [Q8GJ44] Domain organization of [XYNA1_CLOSR] by SWISSPFAM Domain found in 1OD3: [CBD_IV ] by SMART

Other resources with information on 1OD3

Community annotation for 1OD3 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---