Research workbench
The crystal structure of 6-phosphogluconate dehydrogenase from geobacter metallireducens
Analyse The crystal structure of 6-phosphogluconate dehydrogenase from geobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E21
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase (decarboxylating)
- EC
- 1.1.1.44
- UniProt
- Q39SD5
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44) | protein | 311 | 54% helix, 12% strand | Q39SD5 |
| B | 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44) | protein | 317 | 54% helix, 12% strand | Q39SD5 |
Ligands and binding sites
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.64 | 0.79 | 47 | empty |
| 2 | 245 | 0.55 | 0.77 | 26 | empty |
| 3 | 303 | 0.54 | 0.75 | 25 | empty |
| 4 | 113 | 0.39 | 0.75 | 27 | MRD |
| 5 | 90 | 0.38 | 0.77 | 19 | MRD |
Interfaces
1 interface between chains.
- A–B · 3962 Ų buried · 60 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4E21 · The crystal structure of 6-phosphogluconate dehydrogenase from Geobacter metallireducens · 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 Q39SD5
- Elsewhere: RCSB PDB 4E21 · PDBe 4E21 · UniProt Q39SD5
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