Research workbench
Structure of the H477R variant of rat cytosolic pepck in complex with phosphoglycolate and GDP.
Analyse Structure of the H477R variant of rat cytosolic pepck in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V9H
- Type
- protein
- Length
- 1,220 residues
- Chains
- 2
- 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
- GDP, PGA, MN, NA
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 611 | 29% helix, 24% strand | P07379 |
| B | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 609 | 30% helix, 24% strand | P07379 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- PGA · 2-phosphoglycolic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.77 | 0.81 | 88 | empty |
| 2 | 490 | 0.70 | 0.80 | 68 | MN, GDP, PGA |
| 3 | 328 | 0.68 | 0.82 | 45 | MN, GDP, PGA |
| 4 | 159 | 0.60 | 0.83 | 20 | empty |
| 5 | 143 | 0.58 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 637 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5V9H · Structure of the H477R variant of rat cytosolic PEPCK in complex with phosphoglycolate… · 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 5V9H · PDBe 5V9H · UniProt P07379
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