9HKU | pdb_00009hku

Crystal structure of CREBBP histone acetyltransferase domain in complex with Acetyl-Coenzyme A

PDB DOI: https://doi.org/10.2210/pdb9HKU/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-12-04 Released: 2025-12-17
Deposition Author(s): Mechaly, A.E., Zhang, W., Cui, G., Green, M.R., Rodrigues-Lima, F.
Funding Organization(s): Centre National de la Recherche Scientifique (CNRS), National Institutes of Health/National Cancer Institute (NIH/NCI), Chinese Scholarship Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.287 (Depositor), 0.266 (DCC)
R-Value Work:
0.245 (Depositor)
R-Value Observed:
0.248 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of CREBBP histone acetyltransferase domain in complex with Acetyl-Coenzyme A

Mechaly, A.E., Zhang, W., Cui, G., Green, M.R., Rodrigues-Lima, F.

To be published.

Macromolecule Content

Total Structure Weight: 152.25 kDa
Atom Count: 9,160
Modeled Residue Count: 1,056
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histone acetyltransferase	A, B	640	Mus musculus	Mutation(s): 1 Gene Names: Crebbp EC: 2.3.1.48
UniProt
Find proteins for F8VPR5 (Mus musculus) Explore F8VPR5 Go to UniProtKB: F8VPR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8VPR5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.287 (Depositor), 0.266 (DCC)
R-Value Work: 0.245 (Depositor)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.622	α = 90
b = 139.928	β = 90
c = 154.571	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Centre National de la Recherche Scientifique (CNRS)	France	--
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--
Chinese Scholarship Council	China	--