MolNFT v1 · #110135 · protein
Crystal structure of yeast N-terminal acetyltransferase nate (IP6) in complex with a bisubstrate
4XNH · N-terminal acetyltransferase a complex subunit NAT1: “Crystal structure of yeast N-terminal acetyltransferase nate (IP6) in complex with a bisubstrate”. X-ray diffraction, 3 ligands (IHP, ACO, CMC), 16 pockets (best druggability…
- PDB
- 4XNH
- Type
- protein
- Length
- 1,148 residues
- Chains
- 4
- 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
- IHP, ACO, CMC
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 61% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-terminal acetyltransferase a complex subunit NAT1 | protein | 786 | 76% helix, 0% strand | P12945 |
| B | N-terminal acetyltransferase a complex catalytic subunit ARD1 (EC 2.3.1.88) | protein | 197 | 31% helix, 27% strand | P07347 |
| C | N-terminal acetyltransferase a complex subunit NAT5 (EC 2.3.1.-) | protein | 159 | 30% helix, 38% strand | Q08689 |
| F | ACYH8 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · chains A, B
- ACO · Acetyl coenzyme *A · ligand · chains C
- CMC · Carboxymethyl coenzyme *A · ligand · chains B, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.85 | 0.86 | 95 | CMC |
| 2 | 323 | 0.75 | 0.87 | 41 | IHP |
| 3 | 552 | 0.73 | 0.81 | 52 | empty |
| 4 | 181 | 0.67 | 0.86 | 45 | empty |
| 5 | 399 | 0.66 | 0.79 | 40 | ACO |
Interfaces
5 interfaces between chains.
- A–B · 3956 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 686 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 436 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 360 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 52 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4XNH · Crystal structure of yeast N-terminal acetyltransferase NatE (IP6) in complex with a… · the same entry in another collection · chain F against F, TM-score 1.00
- P12945 · AlphaFold monomer V2.0 prediction for N-terminal acetyltransferase a complex subunit NAT1… · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q08689 · AlphaFold monomer V2.0 prediction for N-alpha-acetyltransferase NAT5 (Q08689) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P07347 · AlphaFold monomer V2.0 prediction for N-terminal acetyltransferase a complex catalytic… · a predicted model of the same protein · chain B against A, TM-score 0.90
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 4XNH · PDBe 4XNH · UniProt P12945 · UniProt P07347 · UniProt Q08689
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