MolNFT v1 · #104299 · protein
Crystal structure of human BAZ2A phd zinc finger in complex with unmodified H3K4 histone peptide
4Q6F · Bromodomain adjacent to zinc finger domain protein 2A: “Crystal structure of human BAZ2A phd zinc finger in complex with unmodified H3K4 histone peptide”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.58). MolNFT…
- 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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