MolNFT v1 · #179689 · protein
Crystal structure of human natd (NAA40) bound to a bisubstrate analogue
7KD7 · N-alpha-acetyltransferase 40: “Crystal structure of human natd (NAA40) bound to a bisubstrate analogue”. X-ray diffraction, 3 ligands (CMC, SO4, NH2), 4 pockets (best druggability 0.73). MolNFT v1 #179689 on GenesisL1: 3D structure…
- PDB
- 7KD7
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 40; Ser-gly-arg-gly-lys
- EC
- 2.3.1.257
- UniProt
- Q86UY6
- Ligands
- CMC, SO4, NH2
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | N-alpha-acetyltransferase 40 (EC 2.3.1.257) | protein | 202 | 41% helix, 28% strand | Q86UY6 |
| E, B | Ser-gly-arg-gly-lys | protein | 5 | 0% helix, 0% strand | — |
| A | N-alpha-acetyltransferase 40 (EC 2.3.1.257) | protein | 204 | 43% helix, 29% strand | Q86UY6 |
Ligands and binding sites
- CMC · Carboxymethyl coenzyme *A · ligand · 2 copies · chains D, E, A, B
- SO4 · Sulfate ion · ion · 4 copies · chains D, A
- NH2 · Amino group · ion · 2 copies · chains D, E, A, B
- GOL · Glycerol · additive · 4 copies · chains D, A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.73 | 0.81 | 53 | GOL |
| 2 | 233 | 0.63 | 0.82 | 29 | CMC |
| 3 | 218 | 0.61 | 0.81 | 27 | CMC |
| 4 | 57 | 0.29 | 0.74 | 11 | GOL |
Interfaces
3 interfaces between chains.
- D–A · 585 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 459 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 450 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KD7 · Crystal structure of human NatD (NAA40) bound to a bisubstrate analogue · the same entry in another collection · chain D against D, TM-score 1.00
- Q86UY6 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 40 (Q86UY6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7KD7 · PDBe 7KD7 · UniProt Q86UY6
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