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Crystal structure of the bromodomain of human BRD1
Analyse Crystal structure of the bromodomain of human BRD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RCW
- Type
- protein
- Length
- 907 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 1
- UniProt
- O95696
- Ligands
- MB3
- Pockets
- 15 · best druggability 0.66
Structure
x-ray diffraction · 7 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 1 | protein | 117 | 65% helix, 0% strand | O95696 |
| B | Bromodomain-containing protein 1 | protein | 118 | 65% helix, 0% strand | O95696 |
| C | Bromodomain-containing protein 1 | protein | 111 | 66% helix, 0% strand | O95696 |
| D, G | Bromodomain-containing protein 1 | protein | 112 | 66% helix, 0% strand | O95696 |
| E | Bromodomain-containing protein 1 | protein | 116 | 66% helix, 0% strand | O95696 |
| F | Bromodomain-containing protein 1 | protein | 113 | 65% helix, 0% strand | O95696 |
| H | Bromodomain-containing protein 1 | protein | 108 | 64% helix, 0% strand | O95696 |
Ligands and binding sites
- MB3 · 1-methylpyrrolidin-2-one · ligand · chains C
- ACT · Acetate ion · additive · 2 copies · chains D, H
- EDO · 1,2-ethanediol · additive · 2 copies · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.66 | 0.78 | 50 | empty |
| 2 | 537 | 0.65 | 0.76 | 40 | empty |
| 3 | 116 | 0.62 | 0.87 | 23 | empty |
| 4 | 217 | 0.59 | 0.80 | 26 | empty |
| 5 | 142 | 0.55 | 0.81 | 20 | empty |
Interfaces
9 interfaces between chains.
- B–G · 499 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 484 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 408 Ų buried · 3 hydrogen bonds · protein-protein
- B–H · 352 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 345 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 O95696
- Elsewhere: RCSB PDB 3RCW · PDBe 3RCW · UniProt O95696
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