7BBO | pdb_00007bbo

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P212121

PDB DOI: https://doi.org/10.2210/pdb7BBO/pdb

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

Deposited: 2020-12-18 Released: 2021-03-03
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., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free:
0.226 (Depositor), 0.217 (DCC)
R-Value Work:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P21212

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: 30.99 kDa
Atom Count: 2,279
Modeled Residue Count: 245
Deposited Residue Count: 256
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH-interacting protein	A [auth AAA], B [auth BBB]	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WWQ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth AAA] SDF format, chain H [auth BBB] SDF format, chain I [auth BBB] SDF format, chain J [auth BBB] SDF format, chain K [auth BBB] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] SDF format, chain N [auth BBB] SDF format, chain E [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain H [auth BBB] MOL2 format, chain I [auth BBB] MOL2 format, chain J [auth BBB] MOL2 format, chain K [auth BBB] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB] MOL2 format, chain N [auth BBB] MOL2 format, chain E [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain H [auth BBB] mmCIF format, chain I [auth BBB] mmCIF format, chain J [auth BBB] mmCIF format, chain K [auth BBB] mmCIF format, chain L [auth BBB] mmCIF format, chain M [auth BBB] mmCIF format, chain N [auth BBB] mmCIF format, chain E [auth AAA]	D [auth AAA] E [auth AAA] H [auth BBB] I [auth BBB] J [auth BBB] D [auth AAA], E [auth AAA], H [auth BBB], I [auth BBB], J [auth BBB], K [auth BBB], L [auth BBB], M [auth BBB], N [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB] Interactions & Density Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain H [auth BBB] Focus chain I [auth BBB] Focus chain J [auth BBB] Focus chain K [auth BBB] Focus chain L [auth BBB] Focus chain M [auth BBB] Focus chain N [auth BBB]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain F [auth BBB] SDF format, chain G [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain F [auth BBB] MOL2 format, chain G [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain F [auth BBB] mmCIF format, chain G [auth BBB]	C [auth AAA], F [auth BBB], G [auth BBB]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth AAA] Focus chain F [auth BBB] Focus chain G [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain F [auth BBB] Focus chain G [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.32 Å
R-Value Free: 0.226 (Depositor), 0.217 (DCC)
R-Value Work: 0.186 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.726	α = 90
b = 56.477	β = 90
c = 91.79	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-03-03

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2021-03-03
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Derived calculations, Refinement description