Research workbench
The 6-phosphogluconate dehydrogenase (NADP-bound) from staphylococcus aureus
Analyse The 6-phosphogluconate dehydrogenase (NADP-bound) 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
- 7CB2
- Type
- protein
- Length
- 1,864 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
- NAP, NO3
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 466 | 57% helix, 10% strand | A0A0H3KGN1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 3 copies · chains A, B, C
- CIT · Citric acid · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.76 | 0.79 | 84 | NO3 |
| 2 | 856 | 0.74 | 0.78 | 84 | empty |
| 3 | 57 | 0.72 | 0.98 | 23 | empty |
| 4 | 391 | 0.70 | 0.82 | 42 | NAP, CIT |
| 5 | 356 | 0.66 | 0.80 | 34 | CIT |
Interfaces
4 interfaces between chains.
- C–D · 5475 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 5377 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 1137 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7CB2 · The 6-phosphogluconate dehydrogenase (NADP-bound) from Staphylococcus aureus · 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 7CB2 · PDBe 7CB2 · UniProt A0A0H3KGN1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.