4Y03 | pdb_00004y03

Crystal Structure of the fifth bromodomain of human PB1 in complex with salicylic acid

PDB DOI: https://doi.org/10.2210/pdb4Y03/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-05 Released: 2015-05-20
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Fedorov, O., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.281 (Depositor), 0.285 (DCC)
R-Value Work:
0.232 (Depositor), 0.229 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4Y03

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

Literature

Crystal Structure of the fifth bromodomain of human PB1 in complex with salicylic acid

Filippakopoulos, P., Picaud, S., Felletar, I., Fedorov, O., von Delft, F., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 29.76 kDa
Atom Count: 2,042
Modeled Residue Count: 230
Deposited Residue Count: 248
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein polybromo-1	A, B	124	Homo sapiens	Mutation(s): 0 Gene Names: PBRM1, BAF180, PB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q86U86 (Homo sapiens) Explore Q86U86 Go to UniProtKB: Q86U86
PHAROS: Q86U86 GTEx: ENSG00000163939
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86U86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
SAL Query on SAL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	2-HYDROXYBENZOIC ACID C₇ H₆ O₃ YGSDEFSMJLZEOE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.281 (Depositor), 0.285 (DCC)
R-Value Work: 0.232 (Depositor), 0.229 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.68	α = 90
b = 58.48	β = 90
c = 139.13	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Filippakopoulos, P.

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references

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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.