MolNFT v1 · #160851 · protein
Cryo-EM structure of human NATE/HYPK complex
6PW9 · N-alpha-acetyltransferase 50: “Cryo-EM structure of human NATE/HYPK complex”. Electron microscopy, 3 ligands (ACE, IHP, ACO), 20 pockets (best druggability 0.85). MolNFT v1 #160851 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6PW9
- Type
- protein
- Length
- 1,075 residues
- Chains
- 4
- 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, Q9NX55
- Ligands
- ACE, IHP, ACO
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-alpha-acetyltransferase 50 (EC 2.3.1.258, 2.3.1.-) | protein | 155 | 27% helix, 34% strand | Q9GZZ1 |
| B | N-alpha-acetyltransferase 15, nata auxiliary subunit | protein | 665 | 71% helix, 0% strand | Q9BXJ9 |
| C | N-alpha-acetyltransferase 10 (EC 2.3.1.255) | protein | 160 | 33% helix, 29% strand | P41227 |
| D | Huntingtin-interacting protein K | protein | 95 | 55% helix, 0% strand | Q9NX55 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, C
- IHP · Inositol hexakisphosphate · ligand · chains B, C
- ACO · Acetyl coenzyme *A · ligand · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.85 | 0.86 | 91 | ACO |
| 2 | 651 | 0.73 | 0.80 | 74 | empty |
| 3 | 965 | 0.72 | 0.76 | 85 | IHP |
| 4 | 583 | 0.70 | 0.79 | 52 | empty |
| 5 | 51 | 0.69 | 0.97 | 21 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2502 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1522 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 774 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 414 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6PW9 · Cryo-EM structure of human NatE/HYPK complex · the same entry in another collection · chain D against D, TM-score 1.00
- 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 0.97
- 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 0.97
- 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 0.94
- Q9NX55 · AlphaFold monomer V2.0 prediction for huntingtin-interacting protein K (Q9NX55) · a predicted model of the same protein · chain D against A, TM-score 0.59
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
- Every structure of UniProt Q9NX55
- Elsewhere: RCSB PDB 6PW9 · PDBe 6PW9 · UniProt Q9GZZ1 · UniProt Q9BXJ9 · UniProt P41227 · UniProt Q9NX55
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