2D8L	Hydrolase	date	Dec 06, 2005
title	Crystal Structure Of Unsaturated Rhamnogalacturonyl Hydrolas Complex With Dglca-Galnac
authors	T.Itoh, A.Ochiai, B.Mikami, W.Hashimoto, K.Murata
compound		source
Molecule: Putative Glycosyl Hydrolase Yter Chain: A Synonym: Rhamnogalacturonyl Hydrolase Ec: 3.2.1.- Engineered: Yes		Organism_scientific: Bacillus Subtilis Organism_taxid: 1423 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmide Expression_system_plasmid: Pet21d
symmetry	Space Group: P 61 2 2	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 91.831 91.831 178.865 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.70 Å
ligand	GCD, NGA	enzyme	Hydrolase E.C.3.2.1 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide., Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K, J Mol Biol. 2006 Jul 14;360(3):573-85. Epub 2006 May 9. PMID:16781735

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk] Biological Unit Coordinates (2d8l.pdb1.gz) 73 Kb LPC: Ligand-Protein Contacts for 2D8L CSU: Contacts of Structural Units for 2D8L Likely Quarternary Molecular Structure file(s) for 2D8L Structure Factors (457 Kb) Retrieve 2D8L in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D8L from S2C, [Save to disk] Re-refined 2d8l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D8L 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 2D8L

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2D8L, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d8l] [2d8l_A] SWISS-PROT database: [O34559] Domain organization of [URHG2_BACSU] by SWISSPFAM

Other resources with information on 2D8L

Community annotation for 2D8L 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

---