Research workbench
Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with diadenosine tetraphosphate (Ap4A)
Analyse Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E20
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Salmonella typhimurium
- Molecule
- Propionate Kinase
- EC
- 2.7.2.15
- UniProt
- O06961
- Ligands
- B4P
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.4 · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Propionate Kinase (EC 2.7.2.15) | protein | 394 | 44% helix, 20% strand | O06961 |
Ligands and binding sites
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.64 | 0.76 | 48 | B4P, EDO |
| 2 | 213 | 0.49 | 0.75 | 23 | empty |
| 3 | 52 | 0.25 | 0.73 | 17 | empty |
Compared structures
- 2E20 · Crystal structure of salmonella typhimurium propionate kinase (tdcd) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- O06961 · AlphaFold monomer V2.0 prediction for propionate kinase (O06961) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 O06961
- Elsewhere: RCSB PDB 2E20 · PDBe 2E20 · UniProt O06961
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