MolNFT v1 · #159931 · protein
The structure of rat cytosolic pepck in complex with 3- (carboxymethylthiol)-picolinic acid
6P5O · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “The structure of rat cytosolic pepck in complex with 3- (carboxymethylthiol)-picolinic acid”. X-ray diffraction, 3 ligands (O2Y, MN, NA), 8 pockets (best druggability 0.73).…
- PDB
- 6P5O
- Type
- protein
- Length
- 619 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
- EC
- 4.1.1.32
- UniProt
- P07379
- Ligands
- O2Y, MN, NA
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 619 | 30% helix, 23% strand | P07379 |
Ligands and binding sites
- O2Y · 3-[(carboxymethyl)sulfanyl]pyridine-2-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.73 | 0.80 | 64 | MN, O2Y |
| 2 | 152 | 0.59 | 0.83 | 20 | empty |
| 3 | 84 | 0.48 | 0.82 | 18 | empty |
| 4 | 62 | 0.38 | 0.80 | 18 | empty |
| 5 | 87 | 0.36 | 0.75 | 19 | empty |
Compared structures
- 6P5O · The structure of rat cytosolic PEPCK in complex with 3-(carboxymethylthiol)-picolinic acid · 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 P07379
- Elsewhere: RCSB PDB 6P5O · PDBe 6P5O · UniProt P07379
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