Research workbench
Pepck mmqx structure 40MS post-mixing with oxaloacetic acid
Analyse Pepck mmqx structure 40MS post-mixing with oxaloacetic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L3M
- Type
- protein
- Length
- 612 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, 2.7.11.-
- UniProt
- P07379
- Ligands
- PEP, GDP, MN, NA, CO2
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32, 2.7.11.-) | protein | 612 | 31% helix, 24% strand | P07379 |
Ligands and binding sites
- PEP · Phosphoenolpyruvate · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 3 copies · chains A
- NA · Sodium ion · metal · chains A
- CO2 · Carbon dioxide · ion · 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 | 404 | 0.70 | 0.82 | 54 | MN, PEP, GDP, CO2 |
| 2 | 163 | 0.57 | 0.81 | 20 | empty |
| 3 | 57 | 0.50 | 0.87 | 18 | empty |
| 4 | 82 | 0.45 | 0.80 | 16 | empty |
| 5 | 77 | 0.37 | 0.76 | 17 | empty |
Compared structures
- 7L3M · PEPCK MMQX structure 40ms post-mixing with oxaloacetic 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 7L3M · PDBe 7L3M · UniProt P07379
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