1VD6	Hydrolase	date	Mar 18, 2004
title	Crystal Structure Of Glycerophosphoryl Diester Phosphodieste Complexed With Glycerol
authors	J.Ishijima, K.Yutani, Riken Structural Genomicsproteomics Ini (Rsgi)
compound		source
Molecule: Glycerophosphoryl Diester Phosphodiesterase Chain: A Ec: 3.1.4.46 Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11a
symmetry	Space Group: P 32 2 1	R_factor 0.217 R_Free 0.233
crystal cell	length a length b length c angle alpha angle beta angle gamma 74.194 74.194 73.439 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.30 Å
ligand	GOL	enzyme	Hydrolase E.C.3.1.4.46 BRENDA
related structures	by homologous chain: 1V8E
Gene Ontology	Chain Function Process Component A

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk] Biological Unit Coordinates (1vd6.pdb1.gz) 80 Kb LPC: Ligand-Protein Contacts for 1VD6 CSU: Contacts of Structural Units for 1VD6 Likely Quarternary Molecular Structure file(s) for 1VD6 Structure Factors (842 Kb) Retrieve 1VD6 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VD6 from S2C, [Save to disk] Re-refined 1vd6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VD6 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 1VD6

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 1VD6, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1vd6] [1vd6_A] SWISS-PROT database: [Q53W25] Domain organization of [Q53W25_THET8] by SWISSPFAM

Other resources with information on 1VD6

Community annotation for 1VD6 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

---