MolNFT v1 · #97990 · protein
The nata (NAA10P/NAA15P) amino-terminal acetyltrasferase complex bound to accoa
4KVO · N-terminal acetyltransferase a complex subunit NAT1: “The nata (NAA10P/NAA15P) amino-terminal acetyltrasferase complex bound to accoa”. X-ray diffraction, 4 ligands (ACO, NA, CL), 20 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 4KVO
- Type
- protein
- Length
- 3,486 residues
- Chains
- 8
- 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
- UniProt
- O74985, Q9UTI3
- Ligands
- ACO, NA, CL, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 69% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-terminal acetyltransferase a complex subunit NAT1 | protein | 718 | 72% helix, 0% strand | O74985 |
| B | N-terminal acetyltransferase a complex subunit NAT1 | protein | 722 | 71% helix, 0% strand | O74985 |
| C, D | N-terminal acetyltransferase a complex subunit NAT1 | protein | 717 | 72% helix, 0% strand | O74985 |
| E, F, G, H | N-terminal acetyltransferase a complex catalytic subunit ARD1 (EC 2.3.1.88) | protein | 153 | 33% helix, 29% strand | Q9UTI3 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 4 copies · chains E, F, G, H
- NA · Sodium ion · metal · 5 copies · chains A, E, D, H, G
- CL · Chloride ion · ion · 63 copies · chains A, B, F, C, D, E, G, 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 993 | 0.80 | 0.82 | 85 | empty |
| 2 | 1160 | 0.79 | 0.80 | 113 | ACO, CL |
| 3 | 684 | 0.78 | 0.83 | 62 | ACO |
| 4 | 713 | 0.74 | 0.80 | 57 | CL |
| 5 | 770 | 0.72 | 0.78 | 68 | CL |
Interfaces
9 interfaces between chains.
- B–F · 2320 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 2289 Ų buried · 28 hydrogen bonds · protein-protein
- C–G · 2278 Ų buried · 25 hydrogen bonds · protein-protein
- D–H · 2266 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1012 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4KVO · The NatA (Naa10p/Naa15p) amino-terminal acetyltrasferase complex bound to AcCoA · the same entry in another collection · chain H against H, TM-score 1.00
- Q9UTI3 · AlphaFold monomer V2.0 prediction for N-terminal acetyltransferase a complex catalytic… · a predicted model of the same protein · chain E against A, TM-score 0.99
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 4KVO · PDBe 4KVO · UniProt O74985 · UniProt Q9UTI3
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