Research workbench
Crystal structure of the bromodomain of human BRD7 bound to TG003
Analyse Crystal structure of the bromodomain of human BRD7 bound to TG003 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V0Q
- Type
- protein
- Length
- 470 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 7
- UniProt
- Q9NPI1
- Ligands
- EAE, PO4, CL
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 7 | protein | 119 | 63% helix, 0% strand | Q9NPI1 |
| B, C, D | Bromodomain-containing protein 7 | protein | 117 | 65% helix, 0% strand | Q9NPI1 |
Ligands and binding sites
- EAE · (1~{Z})-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.79 | 0.89 | 44 | EAE |
| 2 | 74 | 0.74 | 0.98 | 17 | empty |
| 3 | 330 | 0.72 | 0.84 | 45 | EAE |
| 4 | 124 | 0.36 | 0.72 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 849 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 429 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 359 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6V0Q · Crystal structure of the bromodomain of human BRD7 bound to TG003 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9NPI1 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 7 (Q9NPI1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9NPI1
- Elsewhere: RCSB PDB 6V0Q · PDBe 6V0Q · UniProt Q9NPI1
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