2GRP	Ligase	date	Apr 24, 2006
title	Crystal Structure Of Human Rangap1-Ubc9-Y87a
authors	A.A.Yunus, C.D.Lima
compound		source
Molecule: Ubiquitin-Conjugating Enzyme E2 I Chain: A Synonym: Ubiquitin-Protein Ligase I, Ubiquitin Carrier Prot Sumo-1-Protein Ligase, Sumo-1-Conjugating Enzyme, Ubiquitin Protein 9, P18; Ec: 6.3.2.19 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ube2i, Ubc9, Ubce9 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21de3 Codon Plus Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28b
Molecule: Ran Gtpase-Activating Protein 1 Chain: B Fragment: C-Terminal Domain (Residues 419-587) Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Rangap1 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21de3 Codon Plus Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Psmt3
symmetry	Space Group: P 1	R_factor 0.191 R_Free 0.231
crystal cell	length a length b length c angle alpha angle beta angle gamma 39.429 45.092 60.871 71.08 71.11 75.02
method	X-Ray Diffraction	resolution	2.05 Å
ligand		enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A SUMO conjugating enzyme acti... B
Primary reference	Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway., Yunus AA, Lima CD, Nat Struct Mol Biol. 2006 Jun;13(6):491-9. Epub 2006 May 28. PMID:16732283

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk] Biological Unit Coordinates (2grp.pdb1.gz) 55 Kb CSU: Contacts of Structural Units for 2GRP Likely Quarternary Molecular Structure file(s) for 2GRP Structure Factors (172 Kb) Retrieve 2GRP in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2GRP from S2C, [Save to disk] Re-refined 2grp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2GRP 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 2GRP

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 2GRP, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2grp_B] [2grp] [2grp_A] SWISS-PROT database: [P46060] [P63279] Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB. Belongs to the peroxisomal protein importer (ppi) family according to TCDB. Domain organization of [RAGP1_HUMAN] [UBC9_HUMAN] by SWISSPFAM Domain found in 2GRP: [UBCc ] by SMART

Other resources with information on 2GRP

Community annotation for 2GRP at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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