5X3M

crystal structure of p-Ub-S65-NH2

PDB DOI: https://doi.org/10.2210/pdb5X3M/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2017-02-06 Released: 2017-04-05
Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.271
R-Value Work: 0.206
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of p-Ub-S65-NH2 at 1.82 Angstroms resolution

Man, P., Shuai, G., Qian, Q., Lei, L.

To be published.

Macromolecule Content

Total Structure Weight: 17.25 kDa
Atom Count: 1,374
Modelled Residue Count: 149
Deposited Residue Count: 152
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	A	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ubiquitin	B [auth D]	76	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.271
R-Value Work: 0.206
R-Value Observed: 0.210
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.914	α = 81.91
b = 29.969	β = 72.38
c = 39.726	γ = 62.43

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-04-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-05
Type: Initial release
Version 1.1: 2022-02-09
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.