MolNFT v1 · #140545 · protein
Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment
5YE4 · 1A9D7 vh CH1 chain: “Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.65). MolNFT v1 #140545 on GenesisL1: 3D structure, binding…
- PDB
- 5YE4
- Type
- protein
- Length
- 860 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1A9D7 vh CH1 chain; 1A9D7 L chain; Di-acetylated histone H4
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1A9D7 vh CH1 chain | protein | 210 | 9% helix, 51% strand | — |
| B | 1A9D7 L chain | protein | 211 | 5% helix, 52% strand | — |
| C | 1A9D7 vh CH1 chain | protein | 211 | 10% helix, 51% strand | — |
| D | 1A9D7 L chain | protein | 212 | 6% helix, 52% strand | — |
| E, F | Di-acetylated histone H4 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 26 copies · chains A, B, E, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.65 | 0.75 | 52 | ZN |
| 2 | 564 | 0.61 | 0.74 | 63 | empty |
| 3 | 98 | 0.54 | 0.84 | 23 | empty |
| 4 | 99 | 0.41 | 0.77 | 23 | empty |
| 5 | 88 | 0.40 | 0.78 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1707 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1596 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 426 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 425 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 399 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 modified (disulfide, acetylation).
Compared structures
- 5YE4 · Crystal structure of the complex of di-acetylated histone H4 and 1A9D7 Fab fragment · 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
- Elsewhere: RCSB PDB 5YE4 · PDBe 5YE4
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