Research workbench
Phosphotransacetylase from methanosarcina thermophila co- crystallized with coenzyme a
Analyse Phosphotransacetylase from methanosarcina thermophila co- crystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AF4
- Type
- protein
- Length
- 663 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate acetyltransferase
- EC
- 2.3.1.8
- UniProt
- P38503
- Ligands
- COA
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Phosphate acetyltransferase (EC 2.3.1.8) | protein | 332 | 47% helix, 17% strand | P38503 |
| D | Phosphate acetyltransferase (EC 2.3.1.8) | protein | 331 | 45% helix, 16% strand | P38503 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.65 | 0.77 | 43 | COA |
| 2 | 472 | 0.63 | 0.76 | 49 | COA |
| 3 | 234 | 0.59 | 0.80 | 27 | empty |
| 4 | 195 | 0.57 | 0.80 | 27 | empty |
| 5 | 186 | 0.52 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- C–D · 1647 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, oxidation).
Compared structures
- 2AF4 · Phosphotransacetylase from Methanosarcina thermophila co-crystallized with coenzyme A · the same entry in another collection · chain C against C, TM-score 1.00
- P38503 · AlphaFold monomer V2.0 prediction for phosphate acetyltransferase (P38503) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P38503
- Elsewhere: RCSB PDB 2AF4 · PDBe 2AF4 · UniProt P38503
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