MolNFT v1 · #38105 · protein
Pepck complex with a GTP-competitive inhibitor
2GMV · Phosphoenolpyruvate carboxykinase, cytosolic: “Pepck complex with a GTP-competitive inhibitor”. X-ray diffraction, 3 ligands (PEP, UN8, MN), 15 pockets (best druggability 0.86). MolNFT v1 #38105 on GenesisL1: 3D structure, binding…
- PDB
- 2GMV
- Type
- protein
- Length
- 1,204 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase, cytosolic
- EC
- 4.1.1.32
- UniProt
- P35558
- Ligands
- PEP, UN8, MN
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoenolpyruvate carboxykinase, cytosolic (EC 4.1.1.32) | protein | 602 | 30% helix, 23% strand | P35558 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · 2 copies · chains A, B
- UN8 · N-(4-{[3-butyl-1-(2-fluorobenzyl)-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl]methyl}phenyl)-1-methyl-1H-imidazole-4-sulfonamide · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.86 | 0.88 | 83 | empty |
| 2 | 51 | 0.72 | 0.99 | 15 | empty |
| 3 | 54 | 0.72 | 0.98 | 22 | empty |
| 4 | 452 | 0.69 | 0.80 | 48 | MN, PEP |
| 5 | 440 | 0.67 | 0.79 | 44 | MN, PEP |
Interfaces
1 interface between chains.
- A–B · 1022 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2GMV · PEPCK complex with a GTP-competitive inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P35558 · 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 P35558
- Elsewhere: RCSB PDB 2GMV · PDBe 2GMV · UniProt P35558
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