4WHV

E3 ubiquitin-protein ligase RNF8 in complex with Ubiquitin-conjugating enzyme E2 N and Polyubiquitin-B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.3 Å
  • R-Value Free: 0.337
  • R-Value Work: 0.329

Literature

Macromolecules
Sequence Display for 4WHV

Classification: ligase / protein binding

Total Structure Weight: 180150.09

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin-conjugating enzyme E2 N B, E, H, K 160 Homo sapiens EC#: 2.3.2.23 IUBMB
Fragment: unp residues 1-152
Mutation: C87K
Gene Name(s): UBE2N Gene View BLU
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
E3 ubiquitin-protein ligase RNF8 C, D, I, J 149 Homo sapiens EC#: 6.3.2 IUBMB
Fragment: unp residues 345-485
Gene Name(s): RNF8 Gene View KIAA0646
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Polyubiquitin-B A, F, G, L 83 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

C, D, I, J 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: 8.3 Å
  • R-Value Free: 0.337
  • R-Value Work: 0.329
  • Space Group: P 64 2 2

Unit Cell:

Length (Å) Angle (°)
a = 341.38 α = 90.00
b = 341.38 β = 90.00
c = 113.45 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-09-23
  • Released Date: 2015-09-30
  • Deposition author(s): Hodge, C.D., Edwards, R.A., Glover, J.N.M.

Revision History

  • 2016-03-09
    Type: Database references
  • 2016-05-11
    Type: Database references, Structure summary