5AMF | pdb_00005amf

Crystal structure of the bromodomain of human surface epitope engineered BRD1A in complex with 3D Consortium fragment Ethyl 4,5,6,7- tetrahydro-1H-indazole-5-carboxylate (SGC - Diamond I04-1 fragment screening)

PDB DOI: https://doi.org/10.2210/pdb5AMF/pdb

Classification: HISTONE-BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-03-10 Released: 2015-03-18
Deposition Author(s): Pearce, N.M., Fairhead, M., Strain-Damerell, C., Talon, R., Wright, N., Ng, J.T., Bradley, A., Cox, O., Bowkett, D., Collins, P., Brandao-Neto, J., Douangamath, A., Krojer, T., Burgess-Brown, N., Brennan, P., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.175 (Depositor), 0.178 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Bromodomain of Human Surface Epitope Engineered Brd1A in Complex with 3D Consortium Fragment Ethyl 4,5,6,7-Tetrahydro-1H-Indazole-5-Carboxylate

Pearce, N.M., Fairhead, M., Strain-Damerell, C., Talon, R., Wright, N., Ng, J.T., Bradley, A., Cox, O., Bowkett, D., Collins, P., Brandao-Neto, J., Douangamath, A., Krojer, T., Burgess-Brown, N., Brennan, P., Arrowsmith, C.H., Edwards, E., Bountra, C., von Delft, F.

To be published.

Macromolecule Content

Total Structure Weight: 31.72 kDa
Atom Count: 2,292
Modeled Residue Count: 244
Deposited Residue Count: 270
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BROMODOMAIN-CONTAINING PROTEIN 1	A, B	135	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for O95696 (Homo sapiens) Explore O95696 Go to UniProtKB: O95696
PHAROS: O95696 GTEx: ENSG00000100425
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95696
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TWL Query on TWL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ETHYL (5R)-4,5,6,7-TETRAHYDRO-1H-INDAZOLE-5-CARBOXYLATE C₁₀ H₁₄ N₂ O₂ OYSSLPZFSXHQEY-SSDOTTSWSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.175 (Depositor), 0.178 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.55	α = 90
b = 56.33	β = 90
c = 101.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-03-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-03-18
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2019-03-06
Changes: Data collection, Experimental preparation
Version 1.3: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description