2IO1 Protein Binding, Hydrolase date Oct 09, 2006
title Crystal Structure Of Human Senp2 In Complex With Presumo-3
authors D.Reverter, C.D.Lima
compound source
Molecule: Sentrin-Specific Protease 2
Chain: A, C, E
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 3 Precursor
Chain: B, D, F
Synonym: Sumo-3, Ubiquitin-Like Protein Smt3a, Smt3 Homolog
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sumo3, Smt3a, Smt3h1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b
symmetry Space Group: C 2 2 21
R_factor 0.204 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
141.980 143.360 134.120 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand
enzyme Hydrolase E.C.3.4.22 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, E


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] (163 Kb) [Save to disk]
  • Biological Unit Coordinates (2io1.pdb1.gz) 54 Kb
  • Biological Unit Coordinates (2io1.pdb2.gz) 55 Kb
  • Biological Unit Coordinates (2io1.pdb3.gz) 54 Kb
  • CSU: Contacts of Structural Units for 2IO1
  • Likely Quarternary Molecular Structure file(s) for 2IO1
  • Structure Factors (372 Kb)
  • Retrieve 2IO1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2IO1 from S2C, [Save to disk]
  • Re-refined 2io1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2IO1 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 2IO1
  • 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 2IO1, from MSDmotif at EBI
  • Fold representative 2io1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2io1_C] [2io1] [2io1_A] [2io1_B] [2io1_D] [2io1_E] [2io1_F]
  • SWISS-PROT database: [Q9HC62] [P55854]
  • Belongs to the eukaryotic nuclear pore complex (e-npc) family according to TCDB.
  • Domain organization of [SENP2_HUMAN] [SUMO3_HUMAN] by SWISSPFAM
  • Domain found in 2IO1: [UBQ ] by SMART
  • Other resources with information on 2IO1
  • Community annotation for 2IO1 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science