5VGR Hydrolase date Apr 11, 2017
title Human Atlastin-3, Gdp-Bound
authors J.P.O'Donnell, H.Sondermann
compound source
Molecule: Atlastin-3
Chain: A, B
Fragment: Residues 21-442
Ec: 3.6.5.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Atl3
Expression_system: Escherichia Coli K-12
Expression_system_taxid: 83333
Expression_system_strain: Bl21
symmetry Space Group: C 1 2 1
R_factor 0.198 R_Free 0.228
length a length b length c angle alpha angle beta angle gamma
130.666 57.057 143.423 90.00 116.22 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand GDP enzyme Hydrolase E.C.3.6.5 BRENDA
A, B

Primary referenceTiming and Reset Mechanism of GTP Hydrolysis-Driven Conformational Changes of Atlastin., O'Donnell JP, Cooley RB, Kelly CM, Miller K, Andersen OS, Rusinova R, Sondermann H, Structure. 2017 Jul 5;25(7):997-1010.e4. doi: 10.1016/j.str.2017.05.007. Epub, 2017 Jun 9. PMID:28602821
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (266 Kb) [Save to disk]
  • Biological Unit Coordinates (5vgr.pdb1.gz) 141 Kb
  • Biological Unit Coordinates (5vgr.pdb2.gz) 121 Kb
  • LPC: Ligand-Protein Contacts for 5VGR
  • CSU: Contacts of Structural Units for 5VGR
  • Structure Factors (490 Kb)
  • Retrieve 5VGR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VGR from S2C, [Save to disk]
  • Re-refined 5vgr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5VGR 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 5VGR
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5vgr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vgr] [5vgr_A] [5vgr_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VGR
  • Community annotation for 5VGR at PDBWiki (http://pdbwiki.org)

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