MolNFT v1 · #168396 · protein
Crystal structure of human NAA50 in complex with a truncated cofactor derived inhibitor (compound 2)
6WF5 · N-alpha-acetyltransferase 50: “Crystal structure of human NAA50 in complex with a truncated cofactor derived inhibitor (compound 2)”. X-ray diffraction, 3 ligands (ACE, U44, NH2), 3 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 6WF5
- Type
- protein
- Length
- 332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 50; ACE-met-leu-gly-pro-NH2
- EC
- 2.3.1.258, 2.3.1.-
- UniProt
- Q9GZZ1
- Ligands
- ACE, U44, NH2
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 165 | 33% helix, 31% strand | Q9GZZ1 |
| B | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 159 | 32% helix, 32% strand | Q9GZZ1 |
| C, D | ACE-met-leu-gly-pro-NH2 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- U44 · (2R)-2-hydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide · ligand · 2 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.61 | 0.83 | 29 | U44 |
| 2 | 209 | 0.60 | 0.81 | 26 | ACE, U44 |
| 3 | 94 | 0.51 | 0.83 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 462 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 439 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 420 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6WF5 · Crystal structure of human Naa50 in complex with a truncated cofactor derived inhibitor… · 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 B against A, TM-score 0.96
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 6WF5 · PDBe 6WF5 · UniProt Q9GZZ1
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