Research workbench
Crystal structure of phosphoenolpyruvate carboxykinase from actinobaccilus succinogenes in complex with manganese and pyruvate
Analyse Crystal structure of phosphoenolpyruvate carboxykinase from actinobaccilus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YLH
- Type
- protein
- Length
- 524 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase
- EC
- 4.1.1.49
- UniProt
- Q6W6X5
- Ligands
- DT3, PYR, MN, PO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase (EC 4.1.1.49) | protein | 524 | 32% helix, 23% strand | Q6W6X5 |
Ligands and binding sites
- DT3 · (2S,3S)-2,3-dihydroxy-4-sulfanylbutane-1-sulfonate · ligand · chains A
- PYR · Pyruvic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
- FMT · Formic acid · additive · 3 copies · chains A
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 550 | 0.68 | 0.78 | 55 | MN, PO4, BME, PYR |
| 2 | 97 | 0.44 | 0.79 | 21 | PO4 |
Modifications
Observed in the structure: 3 covalent (additive adduct, covalent ligand).
Compared structures
- 1YLH · Crystal Structure of Phosphoenolpyruvate Carboxykinase from Actinobaccilus succinogenes… · the same entry in another collection · 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 Q6W6X5
- Elsewhere: RCSB PDB 1YLH · PDBe 1YLH · UniProt Q6W6X5
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