5EDV

Structure of the HOIP-RBR/UbcH5B~ubiquitin transfer complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.303
  • R-Value Work: 0.249

Literature

Macromolecules
Sequence Display for 5EDV

Classification: LIGASE / TRANSFERASE

Total Structure Weight: 173205.42

Macromolecule Entities
Molecule Chains Length Organism Details
E3 ubiquitin-protein ligase RNF31 A, B 380 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: UNP residues 696-1072
Gene Name(s): RNF31 Gene View ZIBRA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquitin-conjugating enzyme E2 D2 C, D, I 149 Homo sapiens EC#: 2.3.2.23 IUBMB
Mutation: S22R, C85K
Gene Name(s): UBE2D2 Gene View PUBC1 UBC4 UBC5B UBCH4 UBCH5B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Polyubiquitin-B E, F, G, H 76 Homo sapiens Fragment: UNP residues 1-76
Gene Name(s): UBB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.48 Å
  • R-Value Free: 0.303
  • R-Value Work: 0.249
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 104.82 α = 90.00
b = 75.74 β = 95.56
c = 120.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-10-22
  • Released Date: 2016-01-20
  • Deposition author(s): Lechtenberg, B.C., Mace, P.D., Sanishvili, R., Riedl, S.J.

Revision History

  • Version 1_0: 2016-01-20

    Type: Initial release

  • Version 1_1: 2016-02-03

    Type: Derived calculations

  • Version 1_2: 2016-02-10

    Type: Database references

  • Version 1_3: 2017-09-27

    Type: Author supporting evidence, Database references, Derived calculations, Refinement description