Research workbench
Crystal structure of yeast N-terminal acetyltransferase nate (ppgpp) in complex with a bisubstrate
Analyse Crystal structure of yeast N-terminal acetyltransferase nate (ppgpp) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XPD
- Type
- protein
- Length
- 1,122 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
- G4P, ACO, CMC
- Pockets
- 14 · best druggability 0.86
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 | 774 | 74% helix, 0% strand | P12945 |
| B | N-terminal acetyltransferase a complex catalytic subunit ARD1 (EC 2.3.1.88) | protein | 187 | 30% helix, 27% strand | P07347 |
| C | N-terminal acetyltransferase a complex subunit NAT5 (EC 2.3.1.-) | protein | 155 | 32% helix, 37% strand | Q08689 |
| F | Human ACTH8 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · 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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.86 | 0.87 | 108 | CMC |
| 2 | 736 | 0.73 | 0.79 | 62 | empty |
| 3 | 512 | 0.72 | 0.81 | 45 | G4P |
| 4 | 456 | 0.65 | 0.78 | 57 | empty |
| 5 | 402 | 0.64 | 0.78 | 37 | ACO |
Interfaces
5 interfaces between chains.
- A–B · 3441 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 407 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 42 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4XPD · Crystal structure of yeast N-terminal acetyltransferase NatE (ppGpp) in complex with a… · the same entry in another collection · chain A against A, 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 0.98
- 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 0.92
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 4XPD · PDBe 4XPD · UniProt P12945 · UniProt P07347 · UniProt Q08689
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