Research workbench
Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from dyadobacter fermentans
Analyse Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GBJ
- Type
- protein
- Length
- 1,158 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase NAD-binding
- UniProt
- C6VV20
- Ligands
- NA
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phosphogluconate dehydrogenase NAD-binding | protein | 286 | 53% helix, 13% strand | C6VV20 |
| B, D | 6-phosphogluconate dehydrogenase NAD-binding | protein | 290 | 55% helix, 12% strand | C6VV20 |
| C | 6-phosphogluconate dehydrogenase NAD-binding | protein | 292 | 54% helix, 13% strand | C6VV20 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.73 | 0.79 | 82 | NA |
| 2 | 1086 | 0.73 | 0.76 | 78 | empty |
| 3 | 789 | 0.72 | 0.77 | 75 | empty |
| 4 | 596 | 0.70 | 0.79 | 65 | empty |
| 5 | 382 | 0.62 | 0.78 | 32 | NA |
Interfaces
4 interfaces between chains.
- C–D · 471 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 423 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 191 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 modified (engineered).
Compared structures
- 4GBJ · Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter… · 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 C6VV20
- Elsewhere: RCSB PDB 4GBJ · PDBe 4GBJ · UniProt C6VV20
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