Research workbench
Structure of rat cytosolic pepck LD_3G in complex with oxalate and GTP
Analyse Structure of rat cytosolic pepck LD_3G in complex with oxalate and GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GNQ
- 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
- UniProt
- P07379
- Ligands
- GTP, OXL, MN, NA
- Pockets
- 6 · best druggability 0.68
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) | protein | 612 | 31% helix, 24% strand | P07379 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- OXL · Oxalate ion · 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.68 | 0.80 | 53 | GTP, MN, OXL |
| 2 | 176 | 0.60 | 0.82 | 21 | empty |
| 3 | 78 | 0.46 | 0.81 | 17 | empty |
| 4 | 56 | 0.39 | 0.81 | 18 | empty |
| 5 | 98 | 0.37 | 0.75 | 22 | empty |
Compared structures
- 4GNQ · Structure of rat cytosolic PEPCK Ld_3g in complex with oxalate 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 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 4GNQ · PDBe 4GNQ · UniProt P07379
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