4Q0N | pdb_00004q0n

Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand

PDB DOI: https://doi.org/10.2210/pdb4Q0N/pdb

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

Deposited: 2014-04-02 Released: 2014-05-07
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Monteiro, O., Fedorov, O., Chaikuad, A., Yue, W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.214 (Depositor), 0.217 (DCC)
R-Value Work:
0.176 (Depositor), 0.186 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand

Filippakopoulos, P., Picaud, S., Felletar, I., Martin, S., Monteiro, O., Fedorov, O., Chaikuad, A., Yue, W., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 139.67 kDa
Atom Count: 8,215
Modeled Residue Count: 895
Deposited Residue Count: 1,160
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein polybromo-1	A, B, C, D, E A, B, C, D, E, F, G, H	145	Homo sapiens	Mutation(s): 0 Gene Names: BAF180, PB1, PBRM1
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
2XD Query on 2XD Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain W [auth G] SDF format, chain Y [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain W [auth G] MOL2 format, chain Y [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain W [auth G] mmCIF format, chain Y [auth H]	J [auth A] K [auth B] M [auth C] O [auth D] R [auth E] J [auth A], K [auth B], M [auth C], O [auth D], R [auth E], T [auth F], W [auth G], Y [auth H]	(2E)-1-(2-hydroxyphenyl)-3-(2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)prop-2-en-1-one C₁₅ H₁₅ N₃ O₂ JCKBNTULKLTRHY-SOFGYWHQSA-N		Interactions Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain J [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain W [auth G] Focus chain Y [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth E] SDF format, chain N [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D]	I [auth A] L [auth C] N [auth D] P [auth E] Q [auth E] I [auth A], L [auth C], N [auth D], P [auth E], Q [auth E], S [auth F], U [auth G], V [auth G], X [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.214 (Depositor), 0.217 (DCC)
R-Value Work: 0.176 (Depositor), 0.186 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.021	α = 90
b = 136.722	β = 91.4
c = 114.413	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-07

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-05-07
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description