MolNFT v1 · #166298 · protein

BRD3-BD2 in complex with the cyclic peptide 3.2_3

6ULP · Bromodomain-containing protein 3: “BRD3-BD2 in complex with the cyclic peptide 3.2_3”. X-ray diffraction, 2 ligands (ACE, NH2), 2 pockets (best druggability 0.56). MolNFT v1 #166298 on GenesisL1: 3D structure, binding sites and…

PDB: 6ULP
Type: protein
Length: 231 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bromodomain-containing protein 3; Cyclic peptide 3.2_3
UniProt: Q15059
Ligands: ACE, NH2
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 61% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Bromodomain-containing protein 3	protein	110	65% helix, 0% strand	Q15059
B	Bromodomain-containing protein 3	protein	109	62% helix, 0% strand	Q15059
C	Cyclic peptide 3.2_3	protein	12	0% helix, 17% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains B, C
NH2 · Amino group · ion · chains C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	208	0.56	0.78	24	empty
2	72	0.29	0.72	18	empty

Interfaces

3 interfaces between chains.

A–C · 586 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 583 Å² buried · 1 hydrogen bond · protein-protein
A–B · 49 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (covalent ligand, acetylation).

Compared structures

6ULP · BRD3-BD2 in complex with the cyclic peptide 3.2_3 · the same entry in another collection · chain A against A, TM-score 1.00
Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · 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 Q15059
Elsewhere: RCSB PDB 6ULP · PDBe 6ULP · UniProt Q15059

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