5KYC

Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.426 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation.

Ozen, A.Rouge, L.Bashore, C.Hearn, B.R.Skelton, N.J.Dueber, E.C.

(2018) Structure 26: 72-84.e7


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
B
351Homo sapiensMutation(s): 1 
Gene Names: USP7 (HAUSP)
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to Gene View: USP7
Go to UniProtKB:  Q93009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.426 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 116.330α = 90.00
b = 43.540β = 107.55
c = 84.760γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-21 
  • Released Date: 2017-08-09 
  • Deposition Author(s): Rouge, L., Ozen, A.

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references