1VG1	Protein Transport	date	Apr 22, 2004
title	Gdp-Bound Rab7
authors	A.Rak, O.Pylypenko, A.Niculae, K.Pyatkov, R.S.Goody, K.Alexandrov
compound		source
Molecule: Ras-Related Protein Rab-7 Chain: A Fragment: Gtpase Domain Synonym: Ras-Related Protein P23, Ras-Related Protein Brl-R Engineered: Yes		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet19
symmetry	Space Group: C 2 2 21	R_factor 0.187 R_Free 0.247
crystal cell	length a length b length c angle alpha angle beta angle gamma 64.500 103.200 51.700 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.90 Å
ligand	GDP, MG	enzyme
related structures	by homologous chain: 1T91, 1VG8
Gene Ontology	Chain Function Process Component A
Primary reference	Structure of the Rab7:REP-1 complex: insights into the mechanism of Rab prenylation and choroideremia disease., Rak A, Pylypenko O, Niculae A, Pyatkov K, Goody RS, Alexandrov K, Cell 2004 Jun 11;117(6):749-60. PMID:15186776

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk] Biological Unit Coordinates (1vg1.pdb1.gz) 31 Kb LPC: Ligand-Protein Contacts for 1VG1 CSU: Contacts of Structural Units for 1VG1 Likely Quarternary Molecular Structure file(s) for 1VG1 Structure Factors (135 Kb) Retrieve 1VG1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VG1 from S2C, [Save to disk] Re-refined 1vg1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1VG1 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 1VG1

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 1VG1, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vg1a_, region A [Jmol] [rasmolscript] [script source]     - Domain d1h1vg1, region G:412-532 [Jmol] [rasmolscript] [script source]

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1vg1_A] [1vg1] SWISS-PROT database: [P09527] Domain organization of [RAB7A_RAT] by SWISSPFAM Domain found in 1VG1: [RAB ] by SMART

Other resources with information on 1VG1

Community annotation for 1VG1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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