MolNFT v1 · #61696 · protein
The structure of rat cytosolic pepck in complex with oxalate and GTP
3DT4 · Phosphoenolpyruvate carboxykinase, cytosolic [GTP]: “The structure of rat cytosolic pepck in complex with oxalate and GTP”. X-ray diffraction, 4 ligands (OXL, GTP, MN), 18 pockets (best druggability 0.81). MolNFT v1 #61696 on…
- PDB
- 3DT4
- Type
- protein
- Length
- 1,239 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
- OXL, GTP, MN, NA
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 619 | 31% helix, 23% strand | P07379 |
| C | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] (EC 4.1.1.32) | protein | 620 | 30% helix, 23% strand | P07379 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, C
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C
- MN · Manganese (II) ion · metal · 4 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains A, C
- 1PE · Pentaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.81 | 0.83 | 113 | empty |
| 2 | 738 | 0.76 | 0.81 | 58 | empty |
| 3 | 350 | 0.70 | 0.82 | 53 | MN, OXL, GTP |
| 4 | 390 | 0.69 | 0.81 | 62 | MN, OXL, GTP |
| 5 | 143 | 0.59 | 0.83 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 754 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3DT4 · The structure of rat cytosolic PEPCK in complex with oxalate and GTP · the same entry in another collection · chain C against C, 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 3DT4 · PDBe 3DT4 · UniProt P07379
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