6DC6

Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity.

Lv, Z.Williams, K.M.Yuan, L.Atkison, J.H.Olsen, S.K.

(2018) J. Biol. Chem. 293: 18337-18352


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like modifier-activating enzyme 1
A, C
1015Homo sapiensMutation(s): 1 
Gene Names: UBA1 (A1S9T, UBE1)
EC: 6.2.1.45
Find proteins for P22314 (Homo sapiens)
Go to Gene View: UBA1
Go to UniProtKB:  P22314
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, D
80Homo sapiensMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens)
Go to Gene View: RPS27A
Go to UniProtKB:  P62979
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, C
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.14 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 104.999α = 90.00
b = 70.438β = 95.19
c = 188.851γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM115568

Revision History 

  • Version 1.0: 2018-10-10
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references, Structure summary
  • Version 1.2: 2018-12-05
    Type: Data collection, Database references