5S8Q

XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with FMO3D000185a (space group P212121)

PDB DOI: https://doi.org/10.2210/pdb5S8Q/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: 1.50 Å
R-Value Free: 0.242
R-Value Work: 0.179
R-Value Observed: 0.182

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: 31.11 kDa
Atom Count: 2,267
Modelled Residue Count: 243
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A, B	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XLY (Subject of Investigation/LOI) Query on XLY Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	(3R)-3-methyl-1,2,3,4-tetrahydro-5H-1,4-benzodiazepin-5-one C₁₀ H₁₂ N₂ O XOMCUECONFZUOE-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A] E [auth A] I [auth B] J [auth B] K [auth B] D [auth A], E [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], G [auth B], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]