MolNFT v1 · #111626 · protein
Structure of rat cytosolic pepck in complex with 2,3-pyridine dicarboxylic acid
4YWD · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “Structure of rat cytosolic pepck in complex with 2,3-pyridine dicarboxylic acid”. X-ray diffraction, 3 ligands (NTM, MN, NA), 8 pockets (best druggability 0.74). MolNFT v1 #111626…
- PDB
- 4YWD
- Type
- protein
- Length
- 605 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
- NTM, MN, NA
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 605 | 30% helix, 24% strand | P07379 |
Ligands and binding sites
- NTM · Quinolinic 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.74 | 0.80 | 67 | MN, NTM |
| 2 | 157 | 0.61 | 0.84 | 20 | empty |
| 3 | 55 | 0.53 | 0.89 | 16 | empty |
| 4 | 74 | 0.51 | 0.84 | 21 | empty |
| 5 | 72 | 0.39 | 0.78 | 23 | empty |
Compared structures
- 4YWD · Structure of rat cytosolic pepck in complex with 2,3-Pyridine dicarboxylic 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 4YWD · PDBe 4YWD · UniProt P07379
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