4II2

Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg

Structural Biology Knowledgebase: 4II2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4II2

Classification: LIGASE

Total Structure Weight: 141138.28

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin-activating enzyme E1 1 A 1001 Schizosaccharomyces pombe EC#: 6.2.1.45 IUBMB
Fragment: Uba1, UNP residues 13-1012
Gene Name(s): ptr3 SPBC1604.21c SPBC211.09
Ubiquitin-60S ribosomal protein L40 B 83 Schizosaccharomyces pombe Fragment: UNP residues 1-76
Mutation: K6R, K11R, K27R, S28A, K29R, K33R, K48R, S57A, K63R
Gene Name(s): uep1 ubi2 SPAC1805.12c
Ubiquitin-conjugating enzyme E2 4 C 163 Schizosaccharomyces pombe EC#: 6.3.2.19 IUBMB
Mutation: C21S, C107S
Gene Name(s): ubc4 SPBC119.02

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PG0
Query on PG0

A 2-(2-METHOXYETHOXY)ETHANOL
PEG 6000 (Synonym)
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.213
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.60 α = 90.00
b = 111.20 β = 90.00
c = 181.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-19
  • Released Date: 2013-02-13
  • Deposition author(s): Olsen, S.K., Lima, C.D.

Revision History

  • 2013-03-27
    Type: Citation | Details: Citation update