3NKV Protein Transport date Jun 21, 2010
title Crystal Structure Of Rab1b Covalently Modified With Amp At Y
authors M.P.Mueller, H.Peters, W.Blankenfeldt, R.S.Goody, A.Itzen
compound source
Molecule: Ras-Related Protein Rab-1b
Chain: A, B
Fragment: Rab1b-Amp
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab1b, Rab1b_human
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3) Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal
symmetry Space Group: P 1 21 1
R_factor 0.150 R_Free 0.187
length a length b length c angle alpha angle beta angle gamma
34.970 100.589 45.071 90.00 102.43 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand AMP, BA, GNP, MG enzyme
Gene RAB1B (H. sapiens)
A, B

Primary referenceThe Legionella Effector Protein DrrA AMPylates the Membrane Traffic Regulator Rab1b., Muller MP, Peters H, Blumer J, Blankenfeldt W, Goody RS, Itzen A, Science. 2010 Jul 22. PMID:20651120
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (126 Kb) [Save to disk]
  • Biological Unit Coordinates (3nkv.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (3nkv.pdb2.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 3NKV
  • CSU: Contacts of Structural Units for 3NKV
  • Structure Factors (227 Kb)
  • Retrieve 3NKV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NKV from S2C, [Save to disk]
  • Re-refined 3nkv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NKV 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 3NKV
  • 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
  • 3D motif for 3NKV, from MSDmotif at EBI
  • Fold representative 3nkv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nkv] [3nkv_B] [3nkv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NKV: [RAB ] by SMART
  • Other resources with information on 3NKV
  • Community annotation for 3NKV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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