MolNFT v1 · #136963 · protein
Structure of the H477R variant of rat cytosolic pepck in complex with beta sulfopyruvate and GTP.
5V9F · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “Structure of the H477R variant of rat cytosolic pepck in complex with beta sulfopyruvate and GTP.”. X-ray diffraction, 4 ligands (GTP, SPV, MN), 9 pockets (best druggability…
- PDB
- 5V9F
- Type
- protein
- Length
- 611 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, SPV, MN, NA
- Pockets
- 9 · best druggability 0.70
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 | 611 | 30% helix, 24% strand | P07379 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- SPV · Sulfopyruvate · ligand · chains A
- MN · Manganese (II) ion · metal · 3 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 | 419 | 0.70 | 0.82 | 54 | MN, GTP, SPV |
| 2 | 160 | 0.60 | 0.83 | 21 | empty |
| 3 | 76 | 0.52 | 0.85 | 19 | empty |
| 4 | 82 | 0.46 | 0.81 | 16 | empty |
| 5 | 73 | 0.39 | 0.79 | 18 | empty |
Compared structures
- 5V9F · Structure of the H477R variant of rat cytosolic PEPCK in complex with beta sulfopyruvate… · 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 5V9F · PDBe 5V9F · UniProt P07379
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