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 Diffraction	resolution	2.50 Å
ligand	SO4	enzyme	Ligase E.C.6.3.2.19 BRENDA
related structures	by homologous chain: 1A3S, 1U9B
Gene Ontology	Chain Function Process Component A, C SUMO conjugating enzyme acti... D, B
Primary reference	Structural 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

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 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] 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)

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