Research workbench
PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 230)
Analyse PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PVG
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.69
- Source
- Homo sapiens
- Molecule
- Bromodomain-containing protein 1
- UniProt
- O95696
- Ligands
- NA
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.69 · 2 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 1 | protein | 121 | 69% helix, 0% strand | O95696 |
| B | Bromodomain-containing protein 1 | protein | 123 | 68% helix, 0% strand | O95696 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.51 | 0.76 | 22 | EDO |
| 2 | 75 | 0.48 | 0.82 | 19 | EDO |
| 3 | 91 | 0.47 | 0.81 | 17 | EDO |
| 4 | 100 | 0.37 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 5PVG · Pandda analysis group deposition -- crystal structure of BRD1 after initial refinement… · the same entry in another collection · chain A against A, TM-score 1.00
- O95696 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 1 (O95696) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 5PVG · PDBe 5PVG · UniProt O95696
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