5S8M

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N11511a (space group C2)

PDB DOI: https://doi.org/10.2210/pdb5S8M/pdb
Deposition Group: G_1002187 (changed state) ExploreG_1002187

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

Deposited: 2020-12-17 Released: 2021-01-13
Deposition Author(s): Krojer, T., Talon, R., Fairhead, M., Szykowska, A., Burgess-Brown, N.A., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.185
R-Value Work: 0.165
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

XChem group deposition

Krojer, T., Talon, R., Fairhead, M., Szykowska, A., Burgess-Brown, N.A., Brennan, P.E., Arrowsmith, C.H., Edwards, A.M., Bountra, C., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 15.31 kDa
Atom Count: 1,145
Modelled Residue Count: 119
Deposited Residue Count: 128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A	128	Homo sapiens	Mutation(s): 0 Gene Names: PHIP, DCAF14, WDR11
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WWQ0 (Homo sapiens) Explore Q8WWQ0 Go to UniProtKB: Q8WWQ0
PHAROS: Q8WWQ0 GTEx: ENSG00000146247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WWQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1BN (Subject of Investigation/LOI) Query on 1BN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1-BENZYL-1H-IMIDAZOLE C₁₀ H₁₀ N₂ KKKDZZRICRFGSD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.185
R-Value Work: 0.165
R-Value Observed: 0.166
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.91	α = 90
b = 27.35	β = 99.42
c = 56.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-01-13

Deposition Author(s):

Burgess-Brown, N.A.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2021-01-13
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, 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.