1KPS Ligase Protein Transport date Jan 02, 2002
title Structural Basis For E2-Mediated Sumo Conjugation Revealed B Complex Between Ubiquitin Conjugating Enzyme Ubc9 And Ranga
authors V.Bernier-Villamor, D.A.Sampson, M.J.Matunis, C.D.Lima
compound source
Molecule: Ubiquitin-Like Protein Sumo-1 Conjugating Enzyme
Chain: A, C
Synonym: Ubc9, Sumo-1-Protein Ligase, Ubiquitin Carrier Pro
Ec: 6.3.2.19
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubc9
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 (De3) Plys
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ran-Gtpase Activating Protein 1
Chain: B, D
Synonym: Rangap1
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Rangap1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Modified Pet28b-Psumo
symmetry Space Group: P 21 21 2
R_factor 0.223 R_Free 0.300
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.531 126.509 72.639 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand SO4 enzyme Ligase E.C.6.3.2.19 BRENDA
related structures by homologous chain: 1A3S, 1U9B
Gene
Ontology
ChainFunctionProcessComponent
A, C
  • SUMO conjugating enzyme acti...


  • D, B


    Primary referenceStructural basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin-conjugating enzyme Ubc9 and RanGAP1., Bernier-Villamor V, Sampson DA, Matunis MJ, Lima CD, Cell 2002 Feb 8;108(3):345-56. PMID:11853669
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (1kps.pdb1.gz) 58 Kb
  • Biological Unit Coordinates (1kps.pdb2.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 1KPS
  • CSU: Contacts of Structural Units for 1KPS
  • Likely Quarternary Molecular Structure file(s) for 1KPS
  • Structure Factors (240 Kb)
  • Retrieve 1KPS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1KPS from S2C, [Save to disk]
  • Re-refined 1kps structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1KPS 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 1KPS
  • 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 1KPS, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1kpsa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1kpsb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1kpsc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1kpsd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1kps from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1kps_B] [1kps_A] [1kps_C] [1kps_D] [1kps]
  • SWISS-PROT database: [P46061] [P63279]
  • Belongs to the peroxisomal protein importer (ppi) family according to TCDB.
  • Domain organization of [RAGP1_MOUSE] [UBC9_HUMAN] by SWISSPFAM
  • Domain found in 1KPS: [UBCc ] by SMART
  • Other resources with information on 1KPS
  • Community annotation for 1KPS 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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