MolNFT v1 · #110691 · protein
Crystal structure of yeast N-terminal acetyltransferase (ppgpp) nate in complex with a bisubstrate
4Y49 · N-terminal acetyltransferase a complex subunit NAT1: “Crystal structure of yeast N-terminal acetyltransferase (ppgpp) nate in complex with a bisubstrate”. X-ray diffraction, 3 ligands (G4P, CMC, ACO), 20 pockets (best druggability…
- PDB
- 4Y49
- Type
- protein
- Length
- 3,283 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-terminal acetyltransferase a complex subunit NAT1; N-terminal acetyltransferase a…
- EC
- 2.3.1.88, 2.3.1.-
- UniProt
- P12945, P07347, Q08689
- Ligands
- G4P, CMC, ACO
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 38% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-terminal acetyltransferase a complex subunit NAT1 | protein | 769 | 44% helix, 0% strand | P12945 |
| B, H, N | N-terminal acetyltransferase a complex catalytic subunit ARD1 (EC 2.3.1.88) | protein | 164 | 10% helix, 13% strand | P07347 |
| C | N-terminal acetyltransferase a complex subunit NAT5 (EC 2.3.1.-) | protein | 156 | 19% helix, 10% strand | Q08689 |
| E, K, Q | Ala-ala-ala-ala-ala-ala | protein | 6 | 0% helix, 0% strand | — |
| G | N-terminal acetyltransferase a complex subunit NAT1 | protein | 770 | 44% helix, 0% strand | P12945 |
| I | N-terminal acetyltransferase a complex subunit NAT5 (EC 2.3.1.-) | protein | 155 | 15% helix, 3% strand | Q08689 |
| M | N-terminal acetyltransferase a complex subunit NAT1 | protein | 769 | 45% helix, 0% strand | P12945 |
| O | N-terminal acetyltransferase a complex subunit NAT5 (EC 2.3.1.-) | protein | 154 | 16% helix, 6% strand | Q08689 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 3 copies · chains A, B, G, H, M, N
- CMC · Carboxymethyl coenzyme *A · ligand · 3 copies · chains B, E, H, K, N, Q
- ACO · Acetyl coenzyme *A · ligand · 3 copies · chains C, I, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.83 | 0.84 | 151 | CMC |
| 2 | 1113 | 0.82 | 0.83 | 163 | CMC |
| 3 | 1038 | 0.79 | 0.80 | 117 | empty |
| 4 | 1080 | 0.77 | 0.79 | 120 | empty |
| 5 | 1141 | 0.77 | 0.79 | 106 | empty |
Interfaces
11 interfaces between chains.
- M–N · 1807 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 1759 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1743 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 443 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 431 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 4Y49 · Crystal structure of yeast N-terminal acetyltransferase (ppGpp) NatE in complex with a… · the same entry in another collection · chain Q against Q, 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 P12945
- Every structure of UniProt P07347
- Every structure of UniProt Q08689
- Elsewhere: RCSB PDB 4Y49 · PDBe 4Y49 · UniProt P12945 · UniProt P07347 · UniProt Q08689
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.