MolNFT v1 · #160615 · protein
Cryo-EM structure of human nate complex (NATA/NAA50)
6PPL · N-alpha-acetyltransferase 50: “Cryo-EM structure of human nate complex (NATA/NAA50)”. Electron microscopy, 3 ligands (ACO, ACE, IHP), 11 pockets (best druggability 0.84). MolNFT v1 #160615 on GenesisL1: 3D structure, binding sites…
- PDB
- 6PPL
- Type
- protein
- Length
- 980 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-alpha-acetyltransferase 50; N-alpha-acetyltransferase 15, nata auxiliary subunit…
- EC
- 2.3.1.258, 2.3.1.-, 2.3.1.255
- UniProt
- Q9GZZ1, Q9BXJ9, P41227
- Ligands
- ACO, ACE, IHP
- Pockets
- 11 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 155 | 32% helix, 35% strand | Q9GZZ1 |
| B | N-alpha-acetyltransferase 15, nata auxiliary subunit | protein | 665 | 68% helix, 0% strand | Q9BXJ9 |
| C | N-alpha-acetyltransferase 10 (EC 2.3.1.255) | protein | 160 | 34% helix, 29% strand | P41227 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains A, B, C
- ACE · Acetyl group · ligand · chains B, C
- IHP · Inositol hexakisphosphate · ligand · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1033 | 0.84 | 0.85 | 83 | ACO |
| 2 | 618 | 0.71 | 0.79 | 64 | IHP |
| 3 | 408 | 0.68 | 0.80 | 38 | ACO |
| 4 | 325 | 0.63 | 0.80 | 41 | empty |
| 5 | 357 | 0.55 | 0.74 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2517 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 731 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6PPL · Cryo-EM structure of human NatE complex (NatA/Naa50) · the same entry in another collection · chain A against A, TM-score 1.00
- P41227 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 10 (P41227) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q9BXJ9 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 15, nata auxiliary… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q9GZZ1 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase 50 (Q9GZZ1) · a predicted model of the same protein · chain A against A, TM-score 0.97
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
- Every structure of UniProt Q9BXJ9
- Every structure of UniProt P41227
- Elsewhere: RCSB PDB 6PPL · PDBe 6PPL · UniProt Q9GZZ1 · UniProt Q9BXJ9 · UniProt P41227
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