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 Diffractionresolution 2.05 Å
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • SUMO conjugating enzyme acti...


  • B


    Primary referenceLysine 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] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2grp.pdb1.gz) 56 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
  • 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 2GRP, from MSDmotif at EBI
  • Fold representative 2grp from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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