2GZD Protein Transport date May 11, 2006
title Crystal Structure Of Rab11 In Complex With Rab11-Fip2
authors A.R.Khan
compound source
Molecule: Ras-Related Protein Rab-11a
Chain: A, B
Fragment: G Protein Domain
Synonym: Rab-11, Yl8
Ec: 3.6.5.2
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab11a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28b

Molecule: Rab11 Family-Interacting Protein 2
Chain: C, D
Fragment: Rab11-Fip2 Rab-Binding Domain
Synonym: Rab11-Fip2, Nrip11
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-C2x
symmetry Space Group: P 21 21 21
R_factor 0.226 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
64.364 91.149 113.099 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.44 Å
ligand GTP, MG, MSE enzyme Hydrolase E.C.3.6.5.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of rab11 in complex with rab11 family interacting protein 2., Jagoe WN, Lindsay AJ, Read RJ, McCoy AJ, McCaffrey MW, Khan AR, Structure. 2006 Aug;14(8):1273-83. PMID:16905101
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (76 Kb) [Save to disk]
  • Biological Unit Coordinates (2gzd.pdb1.gz) 69 Kb
  • LPC: Ligand-Protein Contacts for 2GZD
  • CSU: Contacts of Structural Units for 2GZD
  • Likely Quarternary Molecular Structure file(s) for 2GZD
  • Structure Factors (377 Kb)
  • Retrieve 2GZD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GZD from S2C, [Save to disk]
  • Re-refined 2gzd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2GZD 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 2GZD
  • 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 2GZD, from MSDmotif at EBI
  • Fold representative 2gzd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gzd_C] [2gzd] [2gzd_B] [2gzd_D] [2gzd_A]
  • SWISS-PROT database: [P62491] [Q7L804]
  • Domain organization of [RB11A_HUMAN] [RFIP2_HUMAN] by SWISSPFAM
  • Domain found in 2GZD: [RAB ] by SMART
  • Alignments of the sequence of 2GZD with the sequences similar proteins can be viewed for 2GZD's classification [RB11A_HUMAN] [RFIP2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [RB11A_HUMAN] [RFIP2_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2GZD
  • Community annotation for 2GZD 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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