Research workbench
The 6-phosphogluconate dehydrogenase from staphylococcus aureus (6- phosphogluconate bound)
Analyse The 6-phosphogluconate dehydrogenase from staphylococcus aureus (6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CB5
- Type
- protein
- Length
- 1,863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, decarboxylating
- EC
- 1.1.1.44
- UniProt
- A0A0H3KGN1
- Ligands
- 6PG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 466 | 57% helix, 10% strand | A0A0H3KGN1 |
| B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 467 | 57% helix, 10% strand | A0A0H3KGN1 |
| D | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 464 | 55% helix, 9% strand | A0A0H3KGN1 |
Ligands and binding sites
- 6PG · 6-phosphogluconic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.76 | 0.80 | 84 | empty |
| 2 | 62 | 0.72 | 0.97 | 15 | empty |
| 3 | 55 | 0.71 | 0.98 | 24 | empty |
| 4 | 185 | 0.69 | 0.87 | 42 | empty |
| 5 | 324 | 0.68 | 0.82 | 37 | 6PG |
Interfaces
4 interfaces between chains.
- C–D · 5414 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 5403 Ų buried · 54 hydrogen bonds · protein-protein
- B–D · 839 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7CB5 · The 6-phosphogluconate dehydrogenase from Staphylococcus aureus (6-phosphogluconate bound) · 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 A0A0H3KGN1
- Elsewhere: RCSB PDB 7CB5 · PDBe 7CB5 · UniProt A0A0H3KGN1
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