Research workbench
Crystal structure of mtb pepck in complex with GDP and metals
Analyse Crystal structure of mtb pepck in complex with GDP and metals in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WOU
- Type
- protein
- Length
- 595 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, MN, ZN, PO4
- Pockets
- 6 · best druggability 0.79
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 | 595 | 32% helix, 22% strand | A5TYT6 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 875 | 0.79 | 0.81 | 88 | GDP, GOL, MN, ZN, PO4 |
| 2 | 69 | 0.75 | 0.99 | 22 | empty |
| 3 | 119 | 0.57 | 0.84 | 20 | empty |
| 4 | 141 | 0.57 | 0.83 | 22 | empty |
| 5 | 59 | 0.30 | 0.75 | 17 | empty |
Compared structures
- 4WOU · Crystal Structure of Mtb PEPCK in complex with GDP and metals · 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 4WOU · PDBe 4WOU · UniProt A5TYT6
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