7B7W

Notum-Fragment049

• PDB DOI: https://doi.org/10.2210/pdb7B7W/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2020-12-11 Released: 2021-07-21 
• Deposition Author(s): Zhao, Y., Jonees, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.227 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Notum Fragment Screen

Zhao, Y., Jones, E.Y.

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

Macromolecule Content

• Total Structure Weight: 44.34 kDa 
• Atom Count: 2,941 
• Modelled Residue Count: 351 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Palmitoleoyl-protein carboxylesterase NOTUM	A	383	Homo sapiens	Mutation(s): 1  Gene Names: NOTUM, OK/SW-CL.30 EC: 3.1.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P988 (Homo sapiens) Explore Q6P988  Go to UniProtKB:  Q6P988
PHAROS:  Q6P988 GTEx:  ENSG00000185269
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q6P988-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
JGA (Subject of Investigation/LOI)	H [auth A]	N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea C7 H11 N3 O2 OLTOJZGRSVNYRB-UHFFFAOYSA-N
SO4	B [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.227 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.003	α = 90
b = 72.68	β = 90
c = 78.475	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-21 
Deposition Author(s): Zhao, Y., Jonees, E.Y.

Revision History  

• Version 1.0: 2021-07-21
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary