Research workbench
Crystal structure of human NAA50 in complex with accoa and an inhibitor (compound 4B) identified using DNA encoded library technology
Analyse Crystal structure of human NAA50 in complex with accoa and an inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WFO
- 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
- ACO, U3Y
- Pockets
- 5 · best druggability 0.68
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, 35% 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
- ACO · Acetyl coenzyme *A · ligand · 3 copies · chains A, B, C
- U3Y · (4S)-1-methyl-N-{(3S,5R)-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
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.68 | 0.82 | 35 | ACO, U3Y |
| 2 | 383 | 0.68 | 0.80 | 44 | ACO, U3Y |
| 3 | 354 | 0.67 | 0.80 | 38 | ACO, U3Y |
| 4 | 400 | 0.65 | 0.79 | 39 | empty |
| 5 | 119 | 0.44 | 0.78 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 596 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 446 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6WFO · Crystal structure of human Naa50 in complex with AcCoA and an inhibitor (compound 4b)… · 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 0.99
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 6WFO · PDBe 6WFO · UniProt Q9GZZ1
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