Research workbench
Crystal structure of phd finger-linker-bromodomain fragment of human bptf in the H3(1-15)K4ME2 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
- 2FSA
- 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(1-15)K4ME2 peptide
- UniProt
- Q7Z7D6
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain phd finger transcription factor | protein | 168 | 51% helix, 6% strand | Q7Z7D6 |
| B | Bromodomain phd finger transcription factor | protein | 167 | 51% helix, 7% strand | Q7Z7D6 |
| C | Bromodomain phd finger transcription factor | protein | 166 | 51% helix, 7% strand | Q7Z7D6 |
| P | Histone H3(1-15)K4ME2 peptide | 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.53 | 0.82 | 23 | empty |
| 2 | 91 | 0.51 | 0.82 | 19 | empty |
| 3 | 101 | 0.50 | 0.82 | 21 | empty |
| 4 | 251 | 0.48 | 0.73 | 31 | empty |
Interfaces
2 interfaces between chains.
- A–P · 523 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 500 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered, methylation).
Compared structures
- 2FSA · 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 2FSA · PDBe 2FSA · UniProt Q7Z7D6
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