8D1T | pdb_00008d1t

Crystal structure of human USP30 in complex with a covalent inhibitor 552 and a Fab

• PDB DOI: https://doi.org/10.2210/pdb8D1T/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): Yes 


• Deposited: 2022-05-27 Released: 2023-02-01 
• Deposition Author(s): Song, X., Butler, J., Li, C., Zhang, K., Zhang, D., Hao, Y.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free: 
  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Models: experimental

Literature

TBD

Song, X., Butler, J., Li, C., Zhang, K., Zhang, D., Hao, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 88.21 kDa 
• Atom Count: 5,608 
• Modeled Residue Count: 710 
• Deposited Residue Count: 785 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 30	A	349	Homo sapiens	Mutation(s): 3  Gene Names: USP30 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q70CQ3 (Homo sapiens) Explore Q70CQ3  Go to UniProtKB:  Q70CQ3
PHAROS:  Q70CQ3 GTEx:  ENSG00000135093

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mouse anti-huUSP30 Fab heavy chain	B [auth H]	222	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mouse anti-huUSP30 Fab light chain	C [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PXW (Subject of Investigation/LOI)	D [auth A]	(1R,2R,4S,7E)-7-[amino(sulfanyl)methylidene]-2-{[(1P)-3-chloro-3'-(1-cyanocyclopropyl)[1,1'-biphenyl]-4-carbonyl]amino}-7-azabicyclo[2.2.1]heptan-7-ium C24 H24 Cl N4 O S QYJCMFNKFUMQPQ-IOMROCGXSA-O
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.94 Å
• R-Value Free:  0.294 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.879	α = 90
b = 71.721	β = 93.98
c = 148.63	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Song, X., Butler, J., Li, C., Zhang, K., Zhang, D., Hao, Y.

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Funding Organization	Location	Grant Number
Other private		Amgen Inc
Other private		Carmot Therapeutics Inc

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary