MolNFT v1 · #104103 · protein

Crystal structure of the fifth bromodomain of human poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand

4Q0N · Protein polybromo-1: “Crystal structure of the fifth bromodomain of human poly-bromodomain containing protein 1 (PB1) in complex…”. X-ray diffraction, 1 ligand (2XD), 10 pockets (best druggability 0.77). MolNFT v1 #104103 on…

PDB: 4Q0N
Type: protein
Length: 895 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein polybromo-1
UniProt: Q86U86
Ligands: 2XD
Pockets: 10 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Protein polybromo-1	protein	113	62% helix, 2% strand	Q86U86
B, C, H	Protein polybromo-1	protein	111	64% helix, 2% strand	Q86U86
D, F, G	Protein polybromo-1	protein	112	63% helix, 2% strand	Q86U86

Ligands and binding sites

2XD · (2E)-1-(2-hydroxyphenyl)-3-(2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)prop-2-en-1-one · ligand · 8 copies · chains A, B, D, C, E, F, G, H
EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, G, D, E, H, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	512	0.77	0.84	60	2XD
2	434	0.77	0.85	49	2XD, EDO
3	436	0.76	0.85	49	2XD, EDO
4	438	0.74	0.83	49	2XD, EDO
5	290	0.57	0.77	29	empty

Interfaces

9 interfaces between chains.

A–F · 774 Å² buried · 12 hydrogen bonds · protein-protein
E–H · 718 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 713 Å² buried · 9 hydrogen bonds · protein-protein
C–G · 654 Å² buried · 8 hydrogen bonds · protein-protein
A–E · 454 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4Q0N · Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1… · the same entry in another collection · chain H against H, TM-score 1.00
Q86U86 · AlphaFold monomer V2.0 prediction for protein polybromo-1 (Q86U86) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q86U86
Elsewhere: RCSB PDB 4Q0N · PDBe 4Q0N · UniProt Q86U86

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