2Y5B

Structure of USP21 in complex with linear diubiquitin-aldehyde

Structural Biology Knowledgebase: 2Y5B SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2Y5B

Classification: PROTEIN BINDING / HYDROLASE

Total Structure Weight: 119175.05

Macromolecule Entities
Molecule Chains Length Organism Details
UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21 A, E 370 Homo sapiens EC#: 3.4.19.12 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 196-565
Gene Name(s): USP21 Gene View USP23 PP1490
UBIQUITIN B, F 152 Homo sapiens Fragment: LINEAR DIUBIQUITIN ALDEHYDE, RESIDUES 1-152
Mutation: G76H
Details: NON-CLEAVABLE LINEAR DIUBIQUITIN ALDEHYDE WITH G76H MUTATION
Gene Name(s): UBB Gene View

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

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

A, E ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
GLZ
Query on GLZ
B, F L-PEPTIDE LINKING C2 H5 N O GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.279
  • R-Value Work: 0.216
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 57.87 α = 90.00
b = 102.20 β = 99.82
c = 86.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-12
  • Released Date: 2012-01-25
  • Deposition author(s): Ye, Y., Akutsu, M., Reyes-Turcu, F., Enchev, R.I., Wilkinson, K.D., Komander, D.

Revision History

No revisions since initial release