Research workbench
Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition
Analyse Structural characterization of a bacterial 6PDH reveals aspects of specificity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IYO
- Type
- protein
- Length
- 470 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, decarboxylating
- EC
- 1.1.1.44
- UniProt
- P96789
- Ligands
- 6PG
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 470 | 56% helix, 10% strand | P96789 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.62 | 0.75 | 31 | empty |
| 2 | 251 | 0.51 | 0.75 | 31 | 6PG |
| 3 | 51 | 0.26 | 0.74 | 13 | empty |
Compared structures
- 2IYO · Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism… · the same entry in another collection · chain A against A, TM-score 1.00
- P96789 · AlphaFold monomer V2.0 prediction for 6-phosphogluconate dehydrogenase, decarboxylating… · 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 P96789
- Elsewhere: RCSB PDB 2IYO · PDBe 2IYO · UniProt P96789
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