Research workbench
Crystal structure of phosphoenolpyruvate carboxykinase of anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions
Analyse Crystal structure of phosphoenolpyruvate carboxykinase of anaerobiospirillum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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