Research workbench
Structure of the H477R variant of rat cytosolic pepck in complex with beta sulfopyruvate and GTP.
Analyse Structure of the H477R variant of rat cytosolic pepck in complex with beta… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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