Research workbench
Crystal structure of amppnp bound propionate kinase (tdcd) from salmonella typhimurium
Analyse Crystal structure of amppnp bound propionate kinase (tdcd) from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X3N
- 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.-
- UniProt
- O06961
- Ligands
- ANP
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Propionate kinase (EC 2.7.2.-) | protein | 394 | 42% helix, 20% strand | O06961 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · 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 | 430 | 0.60 | 0.76 | 37 | EDO |
| 2 | 213 | 0.48 | 0.75 | 20 | empty |
| 3 | 50 | 0.26 | 0.74 | 14 | ANP |
Compared structures
- 1X3N · Crystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium · 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 1X3N · PDBe 1X3N · UniProt O06961
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