Research workbench
Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10
Analyse Crystal structure of the fifth bromodomain of human PB1 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FH6
- Type
- protein
- Length
- 438 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein polybromo-1
- UniProt
- Q86U86
- Ligands
- 5XM
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein polybromo-1 | protein | 111 | 65% helix, 2% strand | Q86U86 |
| C | Protein polybromo-1 | protein | 109 | 64% helix, 0% strand | Q86U86 |
| D | Protein polybromo-1 | protein | 107 | 62% helix, 2% strand | Q86U86 |
Ligands and binding sites
- 5XM · (3~{R})-3-(piperidin-1-ylmethyl)-2,3-dihydro-1~{H}-pyrrolo[1,2-a]quinazolin-5-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.76 | 0.83 | 50 | 5XM |
| 2 | 76 | 0.51 | 0.84 | 16 | 5XM |
| 3 | 66 | 0.48 | 0.84 | 16 | 5XM |
| 4 | 144 | 0.42 | 0.75 | 26 | empty |
| 5 | 62 | 0.30 | 0.74 | 11 | empty |
Interfaces
4 interfaces between chains.
- B–C · 690 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 401 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 154 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FH6 · Crystal structure of the fifth bromodomain of human PB1 in complex with compound 10 · the same entry in another collection · chain A against A, TM-score 1.00
- Q86U86 · AlphaFold monomer V2.0 prediction for protein polybromo-1 (Q86U86) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 5FH6 · PDBe 5FH6 · UniProt Q86U86
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