5FFV | pdb_00005ffv

Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide

PDB DOI: https://doi.org/10.2210/pdb5FFV/pdb

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

Deposited: 2015-12-19 Released: 2015-12-30
Deposition Author(s): Tallant, C., Nunez-Alonso, G., Savitsky, P., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.206 (Depositor), 0.213 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone peptide

Tallant, C., Nunez-Alonso, G., Savitsky, P., Krojer, T., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 30 kDa
Atom Count: 2,244
Modeled Residue Count: 235
Deposited Residue Count: 254
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peregrin	A, B	116	Homo sapiens	Mutation(s): 0 Gene Names: BRPF1, BR140
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201 Go to UniProtKB: P55201
PHAROS: P55201 GTEx: ENSG00000156983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55201
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	C, D	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431 Go to UniProtKB: P68431
PHAROS: P68431 GTEx: ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68431
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY Query on ALY	C, D	L-PEPTIDE LINKING	C₈ H₁₆ N₂ O₃		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.206 (Depositor), 0.213 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)
R-Value Observed: 0.191 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.266	α = 90
b = 74.354	β = 90
c = 49.509	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-12-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-12-30
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary