MolNFT v1 · #111622 · protein
Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid and GTP
4YW9 · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid and GTP”. X-ray diffraction, 4 ligands (GTP, 1WD, MN), 8 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 4YW9
- Type
- protein
- Length
- 614 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
- GTP, 1WD, MN, NA
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 614 | 31% helix, 23% strand | P07379 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- 1WD · 3-sulfanylpyridine-2-carboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- MOH · Methanol · additive · chains A
- 1PE · Pentaethylene glycol · additive · 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 | 399 | 0.68 | 0.80 | 51 | GTP, MN, 1WD |
| 2 | 153 | 0.59 | 0.83 | 21 | empty |
| 3 | 81 | 0.44 | 0.80 | 18 | empty |
| 4 | 63 | 0.37 | 0.79 | 17 | empty |
| 5 | 85 | 0.35 | 0.75 | 20 | empty |
Compared structures
- 4YW9 · Structure of rat cytosolic pepck in complex with 3-mercaptopicolinic acid and GTP · 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 4YW9 · PDBe 4YW9 · UniProt P07379
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.