MolNFT v1 · #28946 · protein
Crystal structure of phosphoenolpyruvate carboxykinase of anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions
1YTM · Phosphoenolpyruvate carboxykinase [ATP]: “Crystal structure of phosphoenolpyruvate carboxykinase of anaerobiospirillum succiniciproducens complexed…”. X-ray diffraction, 4 ligands (ATP, OXD, MG), 7 pockets (best druggability 0.74).…
- PDB
- 1YTM
- Type
- protein
- Length
- 1,034 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase [ATP]
- EC
- 4.1.1.49
- UniProt
- O09460
- Ligands
- ATP, OXD, MG, MN
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) | protein | 517 | 30% helix, 26% strand | O09460 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- OXD · Oxalic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.74 | 0.84 | 59 | MG, MN, ATP, OXD |
| 2 | 341 | 0.70 | 0.83 | 40 | MG, MN, ATP, OXD |
| 3 | 154 | 0.43 | 0.75 | 26 | empty |
| 4 | 85 | 0.41 | 0.79 | 18 | empty |
| 5 | 89 | 0.37 | 0.75 | 20 | empty |
Compared structures
- 1YTM · Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum… · the same entry in another collection · chain A against A, TM-score 1.00
- O09460 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase (ATP) (O09460) · 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 O09460
- Elsewhere: RCSB PDB 1YTM · PDBe 1YTM · UniProt O09460
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