Research workbench
Crystal structure of the fifth bromodomain of human poly-bromodomain containing protein 1 (PB1) in complex with a hydroxyphenyl-propenone ligand
Analyse Crystal structure of the fifth bromodomain of human poly-bromodomain containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q0N
- Type
- protein
- Length
- 895 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein polybromo-1
- UniProt
- Q86U86
- Ligands
- 2XD
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Protein polybromo-1 | protein | 113 | 62% helix, 2% strand | Q86U86 |
| B, C, H | Protein polybromo-1 | protein | 111 | 64% helix, 2% strand | Q86U86 |
| D, F, G | Protein polybromo-1 | protein | 112 | 63% helix, 2% strand | Q86U86 |
Ligands and binding sites
- 2XD · (2E)-1-(2-hydroxyphenyl)-3-(2,4,5,7-tetrahydro-6H-pyrazolo[3,4-c]pyridin-6-yl)prop-2-en-1-one · ligand · 8 copies · chains A, B, D, C, E, F, G, H
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, C, G, D, E, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 512 | 0.77 | 0.84 | 60 | 2XD |
| 2 | 434 | 0.77 | 0.85 | 49 | 2XD, EDO |
| 3 | 436 | 0.76 | 0.85 | 49 | 2XD, EDO |
| 4 | 438 | 0.74 | 0.83 | 49 | 2XD, EDO |
| 5 | 290 | 0.57 | 0.77 | 29 | empty |
Interfaces
9 interfaces between chains.
- A–F · 774 Ų buried · 12 hydrogen bonds · protein-protein
- E–H · 718 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 713 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 654 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 454 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4Q0N · Crystal Structure of the fifth bromodomain of Human Poly-bromodomain containing protein 1… · the same entry in another collection · chain H against H, TM-score 1.00
- Q86U86 · AlphaFold monomer V2.0 prediction for protein polybromo-1 (Q86U86) · a predicted model of the same protein · chain B 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 4Q0N · PDBe 4Q0N · UniProt Q86U86
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