MolNFT v1 · #111621 · protein
Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid
4YW8 · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid”. X-ray diffraction, 4 ligands (1WD, MEE, MN), 10 pockets (best druggability 0.73). MolNFT v1 #111621 on…
- PDB
- 4YW8
- Type
- protein
- Length
- 616 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
- 1WD, MEE, MN, NA
- Pockets
- 10 · 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 | 616 | 30% helix, 23% strand | P07379 |
Ligands and binding sites
- 1WD · 3-sulfanylpyridine-2-carboxylic acid · ligand · 2 copies · chains A
- MEE · Methanethiol · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- MOH · Methanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.73 | 0.79 | 67 | MN, 1WD, MEE |
| 2 | 175 | 0.61 | 0.83 | 24 | empty |
| 3 | 60 | 0.57 | 0.90 | 20 | empty |
| 4 | 84 | 0.46 | 0.81 | 18 | empty |
| 5 | 60 | 0.38 | 0.79 | 18 | empty |
Compared structures
- 4YW8 · Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid · the same entry in another collection · chain A against A, TM-score 1.00
- P07379 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase, cytosolic [GTP]… · 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 P07379
- Elsewhere: RCSB PDB 4YW8 · PDBe 4YW8 · UniProt P07379
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