5H7S Protein Binding Ligase Transferase date Nov 21, 2016
title Structural Basis Of The Flanking Zinc-Finger Motifs Crucial Ligase Activity Of The Lnx1 Ring Domain
authors D.Nayak, J.Sivaraman
compound source
Molecule: Ubiquitin-Like 1
Chain: E, F
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: E3 Ubiquitin-Protein Ligase Lnx
Chain: D, B
Fragment: Unp Residues 11-138
Synonym: Ligand Of Numb-Protein X 1,Numb-Binding Protein 1, Domain-Containing Ring Finger Protein 2,Ring-Type E3 Ubiqui Transferase Lnx;
Ec: 2.3.2.27
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lnx1, Lnx, Pdzrn2, Unq574pro1136
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin-Conjugating Enzyme E2 N
Chain: A, C
Synonym: Bendless-Like Ubiquitin-Conjugating Enzyme,E2 Ubiq Conjugating Enzyme N,Ubc13,Ubch13,Ubiquitin Carrier Protein Ubiquitin-Protein Ligase N;
Ec: 2.3.2.23
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2n, Blu
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.241 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.372 122.372 135.199 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.49 Å
ligand ZN enzyme Transferase E.C.2.3.2.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referenceStructure of LNX1:Ubc13~Ubiquitin complex reveals the role of additional motifs for the E3 ligase activity of LNX1., Nayak D, Sivaraman J, J Mol Biol. 2018 Feb 26. pii: S0022-2836(18)30089-5. doi:, 10.1016/j.jmb.2018.02.016. PMID:29496391
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (247 Kb) [Save to disk]
  • Biological Unit Coordinates (5h7s.pdb1.gz) 239 Kb
  • LPC: Ligand-Protein Contacts for 5H7S
  • CSU: Contacts of Structural Units for 5H7S
  • Structure Factors (413 Kb)
  • Retrieve 5H7S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5H7S from S2C, [Save to disk]
  • View 5H7S 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 5H7S
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5h7s from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5h7s_E] [5h7s_D] [5h7s_B] [5h7s_A] [5h7s_F] [5h7s_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5H7S
  • Community annotation for 5H7S at PDBWiki (http://pdbwiki.org)

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