Research workbench
The apo 6-phosphogluconate dehydrogenase from staphylococcus aureus (strain newman)
Analyse The apo 6-phosphogluconate dehydrogenase from staphylococcus aureus (strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CB0
- Type
- protein
- Length
- 1,862 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
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 466 | 56% helix, 10% strand | A0A0H3KGN1 |
| D | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 464 | 57% helix, 10% strand | A0A0H3KGN1 |
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.80 | 0.83 | 92 | empty |
| 2 | 60 | 0.73 | 0.98 | 22 | empty |
| 3 | 727 | 0.69 | 0.77 | 68 | empty |
| 4 | 743 | 0.68 | 0.75 | 63 | empty |
| 5 | 557 | 0.64 | 0.75 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5330 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 996 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 58 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7CB0 · The apo 6-phosphogluconate dehydrogenase from Staphylococcus aureus (strain Newman) · 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 7CB0 · PDBe 7CB0 · UniProt A0A0H3KGN1
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