5ZBU

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of PA-TM-RING E3 ligase RNF13 RING domain in complex with E2~Ub

Sarkar, S.Datta, A.B.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
C, B
148Homo sapiensMutation(s): 1 
Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B)
EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens)
Go to Gene View: UBE2D2
Go to UniProtKB:  P62837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase RNF13
A, D
76Homo sapiensMutation(s): 0 
Gene Names: RNF13 (RZF)
EC: 2.3.2.27
Find proteins for O43567 (Homo sapiens)
Go to Gene View: RNF13
Go to UniProtKB:  O43567
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
E
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.559α = 90.00
b = 105.740β = 115.49
c = 60.790γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome Trust-DBT India AllianceIndia500241/Z/11/Z

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release