5VBT | pdb_00005vbt

Crystal structure of a highly specific and potent USP7 ubiquitin variant inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5VBT/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-03-30 Released: 2017-06-07 
• Deposition Author(s): DONG, A., DONG, X., LIU, L., GUO, Y., LI, Y., ZHANG, W., WALKER, J.R., SIDHU, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., TONG, Y., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.190 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a highly specific and potent USP7 ubiquitin variant inhibitor

DONG, X., DONG, A., LIU, L., GUO, Y., LI, Y., ZHANG, W., WALKER, J.R., SIDHU, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., TONG, Y., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.75 kDa 
• Atom Count: 1,460 
• Modeled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBH04	A, B	79	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.190 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35VBT

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.011	α = 90
b = 30.83	β = 97.26
c = 51.046	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): DONG, A., DONG, X., LIU, L., GUO, Y., LI, Y., ZHANG, W., WALKER, J.R., SIDHU, S., Bountra, C., Arrowsmith, C.H., Edwards, A.M., TONG, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description