Research workbench
Crystal structure of a phosphotransacetylase from bacillus subtilis
Analyse Crystal structure of a phosphotransacetylase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TD9
- Type
- protein
- Length
- 1,941 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphate acetyltransferase
- EC
- 2.3.1.8
- UniProt
- P39646
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | Phosphate acetyltransferase (EC 2.3.1.8) | protein | 323 | 44% helix, 17% strand | P39646 |
| B | Phosphate acetyltransferase (EC 2.3.1.8) | protein | 324 | 44% helix, 17% strand | P39646 |
| D | Phosphate acetyltransferase (EC 2.3.1.8) | protein | 325 | 44% helix, 17% strand | P39646 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.77 | 0.83 | 114 | SO4 |
| 2 | 274 | 0.68 | 0.84 | 42 | SO4 |
| 3 | 286 | 0.68 | 0.83 | 40 | empty |
| 4 | 399 | 0.66 | 0.80 | 42 | empty |
| 5 | 316 | 0.66 | 0.82 | 40 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1499 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1490 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 676 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 654 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 645 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1TD9 · Crystal Structure of a Phosphotransacetylase from Bacillus subtilis · the same entry in another collection · chain C against C, TM-score 1.00
- P39646 · AlphaFold monomer V2.0 prediction for phosphate acetyltransferase (P39646) · a predicted model of the same protein · chain A 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 P39646
- Elsewhere: RCSB PDB 1TD9 · PDBe 1TD9 · UniProt P39646
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