Research workbench
Crystal structure of the fifth bromodomain of human PB1 in complex with a hydroxyphenyl ligand
Analyse Crystal structure of the fifth bromodomain of human PB1 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E7D
- Type
- protein
- Length
- 444 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein polybromo-1
- UniProt
- Q86U86
- Ligands
- 5KL
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein polybromo-1 | protein | 111 | 65% helix, 2% strand | Q86U86 |
Ligands and binding sites
- 5KL · (2E)-3-(dimethylamino)-1-(2-hydroxyphenyl)prop-2-en-1-one · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.77 | 0.86 | 47 | 5KL |
| 2 | 69 | 0.52 | 0.85 | 15 | 5KL |
| 3 | 76 | 0.48 | 0.82 | 15 | 5KL |
| 4 | 219 | 0.45 | 0.73 | 30 | empty |
| 5 | 94 | 0.42 | 0.78 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–C · 673 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 398 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 190 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5E7D · Crystal Structure of the fifth bromodomain of human PB1 in complex with a hydroxyphenyl… · 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 A 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 5E7D · PDBe 5E7D · UniProt Q86U86
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