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 Diffraction	resolution	2.44 Å
ligand	GTP, MG, MSE	enzyme	Hydrolase E.C.3.6.5.2 BRENDA
Primary reference	Crystal 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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_A] [2gzd_B] [2gzd_C] [2gzd_D] 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)

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