Research workbench
Crystal structure of human BAZ2A phd zinc finger in complex with unmodified H3K4 histone peptide
Analyse Crystal structure of human BAZ2A phd zinc finger in complex with unmodified… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q6F
- Type
- protein
- Length
- 228 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain adjacent to zinc finger domain protein 2A; Unmodified H3K4 peptide
- UniProt
- Q9UIF9
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 6 distinct chains · 17% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain adjacent to zinc finger domain protein 2A | protein | 56 | 21% helix, 14% strand | Q9UIF9 |
| B | Bromodomain adjacent to zinc finger domain protein 2A | protein | 54 | 17% helix, 15% strand | Q9UIF9 |
| C | Bromodomain adjacent to zinc finger domain protein 2A | protein | 51 | 14% helix, 16% strand | Q9UIF9 |
| D | Bromodomain adjacent to zinc finger domain protein 2A | protein | 53 | 17% helix, 15% strand | Q9UIF9 |
| F, G | Unmodified H3K4 peptide | protein | 5 | 0% helix, 20% strand | — |
| H | Unmodified H3K4 peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D, B
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 | 147 | 0.58 | 0.83 | 25 | EDO |
| 2 | 111 | 0.54 | 0.83 | 20 | empty |
| 3 | 57 | 0.49 | 0.85 | 15 | empty |
| 4 | 68 | 0.35 | 0.77 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–D · 745 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 721 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 477 Ų buried · 14 hydrogen bonds · protein-protein
- B–G · 466 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 420 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4Q6F · Crystal structure of human BAZ2A PHD zinc finger in complex with unmodified H3K4 histone… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9UIF9 · AlphaFold monomer V2.0 prediction for bromodomain adjacent to zinc finger domain protein… · a predicted model of the same protein · chain A against A, TM-score 0.89
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 Q9UIF9
- Elsewhere: RCSB PDB 4Q6F · PDBe 4Q6F · UniProt Q9UIF9
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