5D2M Ligase,Protein Binding date Aug 05, 2015
title Complex Between Human Sumo2-Rangap1, Ubc9 And Znf451
authors L.Cappadocia, C.D.Lima
compound source
Molecule: Sumo-Conjugating Enzyme Ubc9
Chain: A, D
Synonym: Sumo-Protein Ligase,Ubiquitin Carrier Protein 9,Ub Carrier Protein I,Ubiquitin-Conjugating Enzyme E2 I,Ubiquit Ligase I,P18;
Ec: 6.3.2.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2i, Ubc9, Ubce9
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Small Ubiquitin-Related Modifier 2
Chain: B, E
Fragment: Unp Residues 15-93
Synonym: Sumo-2,Hsmt3,Smt3 Homolog 2,Sumo-3,Sentrin-2,Ubiqu Protein Smt3b,Smt3b;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sumo2, Smt3b, Smt3h2
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28b

Molecule: Ran Gtpase-Activating Protein 1
Chain: C, F
Fragment: Unp Residues 418-587
Synonym: Rangap1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rangap1, Kiaa1835, Sd
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3

Molecule: Zinc Finger Protein 451
Chain: G
Fragment: Unp Residues 2-56
Synonym: Coactivator For Steroid Receptors
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Znf451, Coaster, Kiaa0576, Kiaa1702
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Plou3
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.240 115.060 130.980 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand EDO enzyme Ligase E.C.6.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D
  • ubiquitin-protein transferas...
  • SUMO conjugating enzyme acti...


  • E, B


    F, C


    Primary referenceStructural basis for catalytic activation by the human ZNF451 SUMO E3 ligase., Cappadocia L, Pichler A, Lima CD, Nat Struct Mol Biol. 2015 Nov 2. doi: 10.1038/nsmb.3116. PMID:26524494
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (413 Kb) [Save to disk]
  • Biological Unit Coordinates (5d2m.pdb1.gz) 248 Kb
  • Biological Unit Coordinates (5d2m.pdb2.gz) 160 Kb
  • LPC: Ligand-Protein Contacts for 5D2M
  • CSU: Contacts of Structural Units for 5D2M
  • Structure Factors (483 Kb)
  • Retrieve 5D2M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D2M from S2C, [Save to disk]
  • Re-refined 5d2m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D2M 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 5D2M
  • 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
  • Fold representative 5d2m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d2m_F] [5d2m_B] [5d2m_E] [5d2m_A] [5d2m_C] [5d2m_G] [5d2m_D] [5d2m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5D2M: [UBCc] [UBQ ] by SMART
  • Other resources with information on 5D2M
  • Community annotation for 5D2M at PDBWiki (http://pdbwiki.org)

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