1K5D	Signaling Protein Signaling Activator	date	Oct 10, 2001
title	Crystal Structure Of Ran-Gppnhp-Ranbp1-Rangap Complex
authors	M.J.Seewald, C.Koerner, A.Wittinghofer, I.R.Vetter
compound		source
Molecule: Gtp-Binding Nuclear Protein Ran Chain: A, D, G, J Synonym: Ran, Tc4, Ran Gtpase, Androgen Receptor-Associated 24; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_plasmid: Pet3d
Molecule: Ran-Specific Gtpase-Activating Protein Chain: B, E, H, K Synonym: Ranbp1, Ran Binding Protein 1 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Bl21 Expression_system_taxid: 511693 Expression_system_strain: Bl21 Expression_system_plasmid: Pgex
Molecule: Ran Gtpase Activating Protein 1 Chain: C, F, I, L Synonym: Rangap, Protein Rna1 Engineered: Yes		Organism_scientific: Schizosaccharomyces Pombe Organism_common: Fission Yeast Organism_taxid: 4896 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: B834 Expression_system_plasmid: Pet3d
symmetry	Space Group: P 1	R_factor 0.237 R_Free 0.267
crystal cell	length a length b length c angle alpha angle beta angle gamma 101.551 103.109 120.177 71.59 80.55 67.78
method	X-Ray Diffraction	resolution	2.70 Å
ligand	GNP, MG	enzyme
related structures	by homologous chain: 1RRP, 1YRG, 2BKU
Gene Ontology	Chain Function Process Component A, J, D, G intracellular transport of v... F, C, I, L GTPase activator activity K, E, B, H GDP-dissociation inhibitor a... GTPase activator activity
Primary reference	RanGAP mediates GTP hydrolysis without an arginine finger., Seewald MJ, Korner C, Wittinghofer A, Vetter IR, Nature 2002 Feb 7;415(6872):662-6. PMID:11832950

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (426 Kb) [Save to disk] Biological Unit Coordinates (1k5d.pdb1.gz) 109 Kb Biological Unit Coordinates (1k5d.pdb2.gz) 109 Kb Biological Unit Coordinates (1k5d.pdb3.gz) 110 Kb Biological Unit Coordinates (1k5d.pdb4.gz) 110 Kb LPC: Ligand-Protein Contacts for 1K5D CSU: Contacts of Structural Units for 1K5D Likely Quarternary Molecular Structure file(s) for 1K5D Structure Factors (1267 Kb) Retrieve 1K5D in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1K5D from S2C, [Save to disk] Re-refined 1k5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1K5D 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 1K5D

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 1K5D, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1k5da_, region A [Jmol] [rasmolscript] [script source]     - Domain d1k5db_, region B [Jmol] [rasmolscript] [script source]     - Domain d1k5dc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1k5dd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1k5de_, region E [Jmol] [rasmolscript] [script source]     - Domain d1k5df_, region F [Jmol] [rasmolscript] [script source]     - Domain d1k5dg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1k5dh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1k5di_, region I [Jmol] [rasmolscript] [script source]     - Domain d1k5dj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1k5dk_, region K [Jmol] [rasmolscript] [script source]     - Domain d1k5dl_, region L [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1k5d_L] [1k5d_F] [1k5d_I] [1k5d_J] [1k5d] [1k5d_G] [1k5d_C] [1k5d_B] [1k5d_K] [1k5d_H] [1k5d_E] [1k5d_D] [1k5d_A] SWISS-PROT database: [P43487] [P62826] [P41391] Belongs to the small nuclear rna exporter (snrna-e) according to TCDB. Domain organization of [RANG_HUMAN] [RAN_HUMAN] [RNA1_SCHPO] by SWISSPFAM Domains found in 1K5D: [LRR] [RAN] [RanBD ] by SMART

Other resources with information on 1K5D

Community annotation for 1K5D at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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