Research workbench
First bromo-adjacent homology (bah) domain of human polybromo-1 (PBRM1)
Analyse First bromo-adjacent homology (bah) domain of human polybromo-1 (PBRM1) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OXB
- Type
- protein
- Length
- 947 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein polybromo-1
- UniProt
- Q86U86
- Ligands
- SO4, CL
- Pockets
- 15 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, F | Protein polybromo-1 | protein | 158 | 8% helix, 51% strand | Q86U86 |
| C | Protein polybromo-1 | protein | 159 | 8% helix, 48% strand | Q86U86 |
| D | Protein polybromo-1 | protein | 157 | 8% helix, 50% strand | Q86U86 |
| E | Protein polybromo-1 | protein | 157 | 8% helix, 50% strand | Q86U86 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 30 copies · chains B, A, C, F, D, E
- CL · Chloride ion · ion · 2 copies · chains B, A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.79 | 0.85 | 58 | empty |
| 2 | 531 | 0.79 | 0.86 | 53 | empty |
| 3 | 477 | 0.79 | 0.86 | 52 | empty |
| 4 | 843 | 0.71 | 0.76 | 75 | empty |
| 5 | 432 | 0.65 | 0.78 | 39 | empty |
Interfaces
8 interfaces between chains.
- D–E · 830 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 795 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 786 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 306 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 98 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6OXB · First bromo-adjacent homology (BAH) domain of human Polybromo-1 (PBRM1) · the same entry in another collection · chain F against F, TM-score 1.00
- Q86U86 · AlphaFold monomer V2.0 prediction for protein polybromo-1 (Q86U86) · a predicted model of the same protein · chain E 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 6OXB · PDBe 6OXB · UniProt Q86U86
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