2IO3 Protein Binding, Hydrolase date Oct 09, 2006
title Crystal Structure Of Human Senp2 In Complex With Rangap1-Sum
authors D.Reverter, C.D.Lima
compound source
Molecule: Sentrin-Specific Protease 2
Chain: A
Fragment: Catalytic Domain
Synonym: Sentrinsumo-Specific Protease Senp2, Smt3-Specifi Isopeptidase 2, Smt3ip2, Axam2;
Ec: 3.4.22.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Senp2, Kiaa1331
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Small Ubiquitin-Related Modifier 2
Chain: B
Synonym: Sumo-2, Ubiquitin-Like Protein Smt3b, Smt3 Homolog Sentrin-2, Hsmt3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sumo2, Smt3b, Smt3h2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ran Gtpase-Activating Protein 1
Chain: C
Fragment: C-Terminal Domain
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rangap1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: P 64 2 2
R_factor 0.277 R_Free 0.306
crystal
cell
length a length b length c angle alpha angle beta angle gamma
164.056 164.056 78.094 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
ligand
enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


C


Primary referenceStructural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates., Reverter D, Lima CD, Nat Struct Mol Biol. 2006 Dec;13(12):1060-8. Epub 2006 Nov 12. PMID:17099700
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (2io3.pdb1.gz) 290 Kb
  • CSU: Contacts of Structural Units for 2IO3
  • Likely Quarternary Molecular Structure file(s) for 2IO3
  • Structure Factors (95 Kb)
  • Retrieve 2IO3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IO3 from S2C, [Save to disk]
  • Re-refined 2io3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IO3 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 2IO3
  • 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 2IO3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2io3] [2io3_A] [2io3_B] [2io3_C]
  • SWISS-PROT database: [P46060] [Q9HC62] [P61956]
  • Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB.
  • Domain organization of [RAGP1_HUMAN] [SENP2_HUMAN] [SUMO2_HUMAN] by SWISSPFAM
  • Domain found in 2IO3: [UBQ ] by SMART
  • Other resources with information on 2IO3
  • Community annotation for 2IO3 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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