MolNFT v1 · #140544 · protein
Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment
5YE3 · 2A7D9 vh CH1 chain: “Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment”. X-ray diffraction, 5 pockets (best druggability 0.61). MolNFT v1 #140544 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YE3
- Type
- protein
- Length
- 433 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2A7D9 vh CH1 chain; 2A7D9 L chain; Di-acetylated histone H4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 2A7D9 vh CH1 chain | protein | 211 | 10% helix, 51% strand | — |
| A | 2A7D9 L chain | protein | 213 | 7% helix, 52% strand | — |
| C | Di-acetylated histone H4 | protein | 9 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.61 | 0.75 | 59 | empty |
| 2 | 145 | 0.41 | 0.74 | 29 | empty |
| 3 | 68 | 0.30 | 0.74 | 16 | empty |
| 4 | 59 | 0.29 | 0.74 | 15 | empty |
| 5 | 58 | 0.29 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1718 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 508 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 323 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 modified (disulfide, acetylation).
Compared structures
- 5YE3 · Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment · the same entry in another collection · chain B against B, 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 5YE3 · PDBe 5YE3
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