7RJL | pdb_00007rjl

Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT

PDB DOI: https://doi.org/10.2210/pdb7RJL/pdb

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

Deposited: 2021-07-21 Released: 2022-08-03
Deposition Author(s): Fedorov, E., Islam, K., Ghosh, A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.185 (Depositor), 0.186 (DCC)
R-Value Work:
0.157 (Depositor), 0.159 (DCC)
R-Value Observed:
0.158 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization

Wagner, S., Fedorov, E., Sudhamalla, B., Jnawali, H.N., Debiec, R., Ghosh, A., Islam, K.

(2021) bioRxiv

DOI: https://doi.org/10.1101/2021.07.28.453719

Macromolecule Content

Total Structure Weight: 31.28 kDa
Atom Count: 2,324
Modeled Residue Count: 243
Deposited Residue Count: 258
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 3	A, B	123	Homo sapiens	Mutation(s): 0 Gene Names: BRD3, KIAA0043, RING3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q15059 (Homo sapiens) Explore Q15059 Go to UniProtKB: Q15059
PHAROS: Q15059 GTEx: ENSG00000169925
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15059
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, cytosolic	C, D	6	Homo sapiens	Mutation(s): 0 EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34896 (Homo sapiens) Explore P34896 Go to UniProtKB: P34896
PHAROS: P34896 GTEx: ENSG00000176974
Entity Groups
UniProt Group	P34896
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [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 A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [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: 1.50 Å
R-Value Free: 0.185 (Depositor), 0.186 (DCC)
R-Value Work: 0.157 (Depositor), 0.159 (DCC)
R-Value Observed: 0.158 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.55	α = 90
b = 61.572	β = 90
c = 83.634	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-03

Deposition Author(s):

Fedorov, E.

Islam, K.

Ghosh, A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM123234
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM130752
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01GM118303

Revision History (Full details and data files)

Version 1.0: 2022-08-03
Type: Initial release
Version 1.1: 2022-08-24
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection
Version 2.1: 2024-11-13
Changes: Structure summary