Research workbench
The silver-bound 6-phosphogluconate dehydrogenase from staphylococcus aureus (strain newman)
Analyse The silver-bound 6-phosphogluconate dehydrogenase from staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CB6
- 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
- AG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 466 | 57% helix, 10% strand | A0A0H3KGN1 |
| C | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 465 | 57% helix, 10% strand | A0A0H3KGN1 |
Ligands and binding sites
- AG · Silver ion · metal · 20 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.74 | 0.81 | 63 | AG |
| 2 | 377 | 0.73 | 0.84 | 35 | empty |
| 3 | 56 | 0.71 | 0.98 | 23 | empty |
| 4 | 56 | 0.71 | 0.98 | 20 | empty |
| 5 | 53 | 0.69 | 0.97 | 24 | empty |
Interfaces
3 interfaces between chains.
- C–D · 5477 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 5420 Ų buried · 61 hydrogen bonds · protein-protein
- B–C · 880 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7CB6 · The silver-bound 6-phosphogluconate dehydrogenase from Staphylococcus aureus (strain… · 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 7CB6 · PDBe 7CB6 · UniProt A0A0H3KGN1
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