Research workbench
Crystal structure of human NAA50 in complex with a cofactor derived inhibitor (compound 1)
Analyse Crystal structure of human NAA50 in complex with a cofactor derived inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WF3
- Type
- protein
- Length
- 924 residues
- Chains
- 12
- 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, COA, NH2
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 150 | 32% helix, 37% strand | Q9GZZ1 |
| G, H, I, J, K, L | ACE-met-leu-gly-pro-NH2 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, L
- COA · Coenzyme A · ligand · 6 copies · chains A, G, B, H, C, I, D, J, E, K, F, L
- NH2 · Amino group · ion · 6 copies · chains G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.71 | 0.80 | 65 | empty |
| 2 | 231 | 0.63 | 0.82 | 30 | COA |
| 3 | 520 | 0.63 | 0.76 | 39 | empty |
| 4 | 233 | 0.63 | 0.82 | 30 | ACE, COA |
| 5 | 227 | 0.63 | 0.82 | 29 | COA |
Interfaces
14 interfaces between chains.
- A–B · 486 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 451 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 415 Ų buried · 6 hydrogen bonds · protein-protein
- F–L · 385 Ų buried · 8 hydrogen bonds · protein-protein
- D–J · 384 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6WF3 · Crystal structure of human Naa50 in complex with a cofactor derived inhibitor (compound 1) · the same entry in another collection · chain L against L, 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 6WF3 · PDBe 6WF3 · UniProt Q9GZZ1
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