MolNFT v1 · #35123 · protein
Crystal structure of salmonella typhimurium propionate kinase (tdcd) in complex with diadenosine tetraphosphate (AP4A)
2E20: “Crystal structure of salmonella typhimurium propionate kinase (tdcd) in complex with diadenosine…”. X-ray diffraction, 1 ligand (B4P), 3 pockets (best druggability 0.64). MolNFT v1 #35123 on GenesisL1: 3D structure, binding sites…
- PDB
- 2E20
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Propionate kinase
- EC
- 2.7.2.15
- UniProt
- O06961
- Ligands
- B4P
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 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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