5QIV

Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102998

• PDB DOI: https://doi.org/10.2210/pdb5QIV/pdb
• Deposition Group: G_1002053 (changed state) ExploreG_1002053

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-10 Released: 2019-12-18 
• Deposition Author(s): Sethi, R., Douangamath, A., Resnick, E., Bradley, A.R., Collins, P., Brandao-Neto, J., Talon, R., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., London, N., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.184 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 

Literature

Covalent fragment group deposition

Sethi, R., Douangamath, A., Resnick, E., Bradley, A.R., Collins, P., Brandao-Neto, J., Talon, R., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., London, N., von Delft, F.

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)

Macromolecule Content

• Total Structure Weight: 26.91 kDa 
• Atom Count: 2,133 
• Modelled Residue Count: 225 
• Deposited Residue Count: 225 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin thioesterase OTUB2	A	225	Homo sapiens	Mutation(s): 0  Gene Names: OTUB2, C14orf137, OTB2, OTU2 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96DC9 (Homo sapiens) Explore Q96DC9  Go to UniProtKB:  Q96DC9
PHAROS:  Q96DC9 GTEx:  ENSG00000089723

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J5P	G [auth A]	N'-acetyl-2-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]acetohydrazide C8 H14 N2 O4 S DIHAZQXZGGBQIS-ZETCQYMHSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNL	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	Unknown ligand LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.184 
• R-Value Work: 0.137 
• R-Value Observed: 0.139 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.24	α = 90
b = 58.635	β = 116.18
c = 49.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Sethi, R., Douangamath, A., Resnick, E., Bradley, A.R., Collins, P., Brandao-Neto, J., Talon, R., Krojer, T., Bountra, C., Arrowsmith, C.H., Edwards, A., London, N., von Delft, F.

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary