4HJK | pdb_00004hjk

U7Ub7 Disulfide variant

PDB DOI: https://doi.org/10.2210/pdb4HJK/pdb

Classification: SIGNALING PROTEIN/Inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2012-10-12 Released: 2012-11-21
Deposition Author(s): Murray, J.M., Rouge, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.217 (Depositor), 0.200 (DCC)
R-Value Work:
0.183 (Depositor), 0.174 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4HJK

This is version 1.2 of the entry. See complete history.

Literature

Potent and selective inhibitors of USP7/HAUSP activity by protein conformational stabilization

Zhang, Y., Zhou, L., Rouge, L., Phillips, A.H., Lam, C., Liu, P., Sandoval, W., Helgason, E., Murray, J.M., Wertz, I., Corn, J.E.

To be published.

Macromolecule Content

Total Structure Weight: 8.81 kDa
Atom Count: 702
Modeled Residue Count: 77
Deposited Residue Count: 77
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	77	Homo sapiens	Mutation(s): 5 Gene Names: DKFZp434K0435, Ubiquitin
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987 Go to UniProtKB: P62987
PHAROS: P62987 GTEx: ENSG00000221983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62987
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.217 (Depositor), 0.200 (DCC)
R-Value Work: 0.183 (Depositor), 0.174 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.197	α = 90
b = 43.197	β = 90
c = 79.154	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XSCALE	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-11-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-11-21
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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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.