Research workbench
Crystal structure of E83A mutant of mtb pepck in complex with pep and GDP
Analyse Crystal structure of E83A mutant of mtb pepck in complex with pep and GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WPU
- Type
- protein
- Length
- 599 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoenolpyruvate carboxykinase [GTP]
- EC
- 4.1.1.32
- UniProt
- A5TYT6
- Ligands
- GDP, PEP
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32) | protein | 599 | 32% helix, 22% strand | A5TYT6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- PEP · Phosphoenolpyruvate · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.69 | 0.82 | 57 | GDP, PEP |
| 2 | 220 | 0.65 | 0.84 | 22 | empty |
| 3 | 172 | 0.58 | 0.82 | 23 | empty |
| 4 | 51 | 0.34 | 0.78 | 15 | empty |
| 5 | 68 | 0.31 | 0.74 | 17 | empty |
Compared structures
- 4WPU · Crystal Structure of E83A mutant of Mtb PEPCK in complex with PEP and GDP · the same entry in another collection · chain A against A, TM-score 1.00
- A5TYT6 · AlphaFold monomer V2.0 prediction for phosphoenolpyruvate carboxykinase [GTP] (A5TYT6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A5TYT6
- Elsewhere: RCSB PDB 4WPU · PDBe 4WPU · UniProt A5TYT6
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