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The nata (NAA10P/NAA15P) amino-terminal acetyltransferase complex bound to a bisubstrate analog
Analyse The nata (NAA10P/NAA15P) amino-terminal acetyltransferase complex bound to a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KVM
- Type
- protein
- Length
- 3,503 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
- 2.3.1.255
- UniProt
- O74985, Q9UTI3
- Ligands
- 1XE, CL, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | N-terminal acetyltransferase a complex subunit NAT1 | protein | 718 | 70% helix, 0% strand | O74985 |
| B | N-terminal acetyltransferase a complex subunit NAT1 | protein | 722 | 71% helix, 0% strand | O74985 |
| C | N-terminal acetyltransferase a complex subunit NAT1 | protein | 717 | 71% helix, 0% strand | O74985 |
| E, F, G, H | N-terminal acetyltransferase a complex catalytic subunit ARD1 (EC 2.3.1.255) | protein | 153 | 35% helix, 29% strand | Q9UTI3 |
| I, J, K, L | Bisubstrate analog inhibitor | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- 1XE · [5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)furan-2-yl]methyl (3R)-4-{[3-({(E)-2-[(2,2-dihydroxyethyl)sulfanyl]ethenyl}amino)-3-oxopropyl]amino}-3-hydroxy-2,2-dimethyl-4-oxobutyl dihydrogen diphosphate · ligand · 4 copies · chains E, I, F, J, G, K, H, L
- CL · Chloride ion · ion · 64 copies · chains A, E, B, F, C, G, D, H
- SO4 · Sulfate ion · ion · 2 copies · chains A, E, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.81 | 0.82 | 111 | CL, 1XE |
| 2 | 900 | 0.80 | 0.82 | 80 | empty |
| 3 | 1046 | 0.78 | 0.80 | 101 | 1XE |
| 4 | 1195 | 0.76 | 0.78 | 98 | CL, 1XE |
| 5 | 1175 | 0.76 | 0.78 | 95 | CL, 1XE |
Interfaces
13 interfaces between chains.
- D–H · 2287 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 2283 Ų buried · 26 hydrogen bonds · protein-protein
- B–F · 2276 Ų buried · 26 hydrogen bonds · protein-protein
- C–G · 2262 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1062 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4KVM · The NatA (Naa10p/Naa15p) amino-terminal acetyltransferase complex bound to a bisubstrate… · 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 O74985
- Every structure of UniProt Q9UTI3
- Elsewhere: RCSB PDB 4KVM · PDBe 4KVM · UniProt O74985 · UniProt Q9UTI3
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