8XPN | pdb_00008xpn

The Crystal Structure of USP8 from Biortus.

PDB DOI: https://doi.org/10.2210/pdb8XPN/pdb

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

Deposited: 2024-01-04 Released: 2024-03-06
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Lin, D., Wang, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.216 (Depositor), 0.223 (DCC)
R-Value Work:
0.176 (Depositor), 0.185 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8XPN

This is version 1.0 of the entry. See complete history.

Literature

The Crystal Structure of USP8 from Biortus.

Wang, F., Cheng, W., Yuan, Z., Lin, D., Wang, J.

To be published.

Macromolecule Content

Total Structure Weight: 130.58 kDa
Atom Count: 8,768
Modeled Residue Count: 1,015
Deposited Residue Count: 1,131
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 8	A, B, C	377	Homo sapiens	Mutation(s): 0 Gene Names: USP8, KIAA0055, UBPY EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P40818 (Homo sapiens) Explore P40818 Go to UniProtKB: P40818
PHAROS: P40818 GTEx: ENSG00000138592
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40818
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain H [auth C] MOL2 format, chain H [auth C] mmCIF format, chain H [auth C]	H [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Interactions & Density Focus chain H [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C]	D [auth A], G [auth B], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain I [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B]	E [auth B], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.216 (Depositor), 0.223 (DCC)
R-Value Work: 0.176 (Depositor), 0.185 (DCC)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.83	α = 90
b = 109.342	β = 90
c = 180.992	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-03-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.