MolNFT v1 · #107423 · protein
Crystal structure of natd bound to H4/H2A peptide and CoA
4U9W · N-alpha-acetyltransferase 40: “Crystal structure of natd bound to H4/H2A peptide and CoA”. X-ray diffraction, 3 ligands (COA, NA, NH2), 12 pockets (best druggability 0.62). MolNFT v1 #107423 on GenesisL1: 3D structure, binding sites…
- PDB
- 4U9W
- Type
- protein
- Length
- 804 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 40; Histone H4/H2A N-terminus
- EC
- 2.3.1.-
- UniProt
- Q86UY6
- Ligands
- COA, NA, NH2
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 40 (EC 2.3.1.-) | protein | 197 | 43% helix, 31% strand | Q86UY6 |
| B | N-alpha-acetyltransferase 40 (EC 2.3.1.-) | protein | 200 | 41% helix, 28% strand | Q86UY6 |
| C | N-alpha-acetyltransferase 40 (EC 2.3.1.-) | protein | 195 | 43% helix, 30% strand | Q86UY6 |
| D | N-alpha-acetyltransferase 40 (EC 2.3.1.-) | protein | 192 | 39% helix, 29% strand | Q86UY6 |
| E, F, G, H | Histone H4/H2A N-terminus | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, F, B, E, C, G, D, H
- NA · Sodium ion · metal · 4 copies · chains A, F, C, G, B, E, D, H
- NH2 · Amino group · ion · 4 copies · chains B, E, A, F, C, G, D, H
- GOL · Glycerol · additive · 4 copies · chains A, F, B, C, G, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.62 | 0.79 | 40 | COA, NA |
| 2 | 278 | 0.62 | 0.80 | 29 | COA, NA |
| 3 | 319 | 0.62 | 0.79 | 36 | COA, NA, GOL |
| 4 | 252 | 0.61 | 0.80 | 24 | GOL |
| 5 | 262 | 0.60 | 0.79 | 30 | COA, NA |
Interfaces
8 interfaces between chains.
- A–B · 757 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 751 Ų buried · 2 hydrogen bonds · protein-protein
- D–H · 459 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 452 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 447 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
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 Q86UY6
- Elsewhere: RCSB PDB 4U9W · PDBe 4U9W · UniProt Q86UY6
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