MolNFT v1 · #168402 · protein
Crystal structure of human NAA50 in complex with CoA and an inhibitor (compound 4A) identified using DNA encoded library technology
6WFK · N-alpha-acetyltransferase 50: “Crystal structure of human NAA50 in complex with CoA and an inhibitor (compound 4A) identified using DNA…”. X-ray diffraction, 2 ligands (COA, U2J), 6 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 6WFK
- Type
- protein
- Length
- 456 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 50
- EC
- 2.3.1.258, 2.3.1.-
- UniProt
- Q9GZZ1
- Ligands
- COA, U2J
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 153 | 32% helix, 36% strand | Q9GZZ1 |
| B | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 152 | 32% helix, 36% strand | Q9GZZ1 |
| C | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 151 | 32% helix, 36% strand | Q9GZZ1 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 3 copies · chains A, B, C
- U2J · (4S)-1-methyl-N-{(3S,5S)-5-[4-(methylcarbamoyl)-1,3-thiazol-2-yl]-1-[4-(1H-tetrazol-5-yl)benzene-1-carbonyl]pyrrolidin-3-yl}-2,6-dioxohexahydropyrimidine-4-carboxamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.67 | 0.81 | 39 | COA, U2J |
| 2 | 354 | 0.67 | 0.80 | 39 | COA, U2J |
| 3 | 324 | 0.66 | 0.81 | 37 | COA, U2J |
| 4 | 363 | 0.63 | 0.78 | 35 | empty |
| 5 | 133 | 0.45 | 0.78 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 605 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 435 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6WFK · Crystal structure of human Naa50 in complex with CoA and an inhibitor (compound 4a)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9GZZ1 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 50 (Q9GZZ1) · a predicted model of the same protein · chain C 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
- Every structure of UniProt Q9GZZ1
- Elsewhere: RCSB PDB 6WFK · PDBe 6WFK · UniProt Q9GZZ1
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