Research workbench
Crystal structure of phd finger-linker-bromodomain fragment of human bptf in the H3(1-15)K4ME3 bound state
Analyse Crystal structure of phd finger-linker-bromodomain fragment of human bptf in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F6J
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain phd finger transcription factor; Histone H3, N-terminal
- UniProt
- Q7Z7D6
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain phd finger transcription factor | protein | 168 | 52% helix, 6% strand | Q7Z7D6 |
| B | Bromodomain phd finger transcription factor | protein | 167 | 51% helix, 8% strand | Q7Z7D6 |
| C | Bromodomain phd finger transcription factor | protein | 166 | 54% helix, 8% strand | Q7Z7D6 |
| P | Histone H3, N-terminal | protein | 6 | 0% helix, 33% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.54 | 0.75 | 33 | empty |
| 2 | 98 | 0.50 | 0.82 | 18 | empty |
| 3 | 106 | 0.50 | 0.81 | 20 | empty |
| 4 | 100 | 0.49 | 0.81 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–P · 540 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 524 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 30 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered, methylation).
Compared structures
- 2F6J · Crystal structure of PHD finger-linker-bromodomain fragment of human BPTF in the… · 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 Q7Z7D6
- Elsewhere: RCSB PDB 2F6J · PDBe 2F6J · UniProt Q7Z7D6
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