Research workbench
Structure of the H477R variant of rat cytosolic pepck in complex with oxalate and GTP.
Analyse Structure of the H477R variant of rat cytosolic pepck in complex with oxalate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V9G
- Type
- protein
- Length
- 620 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
- 9 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 620 | 30% helix, 23% 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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.70 | 0.83 | 53 | MN, GTP, OXL |
| 2 | 148 | 0.58 | 0.82 | 20 | empty |
| 3 | 102 | 0.54 | 0.84 | 23 | empty |
| 4 | 81 | 0.44 | 0.80 | 16 | empty |
| 5 | 55 | 0.38 | 0.80 | 14 | empty |
Compared structures
- 5V9G · Structure of the H477R variant of rat cytosolic PEPCK in complex with oxalate and GTP. · 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 5V9G · PDBe 5V9G · UniProt P07379
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.