Research workbench
Crystal structure of bromodomain of PFA0510W from plasmodium falciparum
Analyse Crystal structure of bromodomain of PFA0510W from plasmodium falciparum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PY6
- Type
- protein
- Length
- 518 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain protein, putative
- UniProt
- Q8I240
- Ligands
- R78
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain protein, putative | protein | 132 | 62% helix, 2% strand | Q8I240 |
| B | Bromodomain protein, putative | protein | 131 | 66% helix, 2% strand | Q8I240 |
| C | Bromodomain protein, putative | protein | 127 | 65% helix, 0% strand | Q8I240 |
| D | Bromodomain protein, putative | protein | 128 | 67% helix, 0% strand | Q8I240 |
Ligands and binding sites
- R78 · 4-{[(7R)-8-cyclopentyl-7-ethyl-5-methyl-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxy-N-(1-methylpiperidin-4-yl)benzamide · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 679 | 0.74 | 0.80 | 42 | EDO |
| 2 | 141 | 0.56 | 0.82 | 25 | R78 |
| 3 | 156 | 0.55 | 0.81 | 20 | R78 |
| 4 | 178 | 0.55 | 0.79 | 27 | R78 |
| 5 | 151 | 0.53 | 0.80 | 22 | R78 |
Interfaces
3 interfaces between chains.
- A–B · 770 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 704 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 655 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4PY6 · Crystal Structure of bromodomain of PFA0510w from Plasmodium Falciparum · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8I240
- Elsewhere: RCSB PDB 4PY6 · PDBe 4PY6 · UniProt Q8I240
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