3PFY

The catalytic domain of human OTUD5

• PDB DOI: https://doi.org/10.2210/pdb3PFY/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-29 Released: 2010-12-15 
• Deposition Author(s): Walker, J.R., Asinas, A.E., Crombet, L., Dong, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Literature

The catalytic domain of human OTUD5

Walker, J.R., Asinas, A.E., Crombet, L., Dong, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Dhe-Paganon, S., 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)

Macromolecule Content

• Total Structure Weight: 22.82 kDa 
• Atom Count: 1,252 
• Modelled Residue Count: 129 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OTU domain-containing protein 5	A	185	Homo sapiens	Mutation(s): 0  Gene Names: OTUD5 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96G74 (Homo sapiens) Explore Q96G74  Go to UniProtKB:  Q96G74
PHAROS:  Q96G74 GTEx:  ENSG00000068308

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	B [auth A], C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	F [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.207 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.605	α = 90
b = 80.605	β = 90
c = 52.263	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Walker, J.R., Asinas, A.E., Crombet, L., Dong, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary