Research workbench
IRED361 from micromonospora sp. in complex with NADP+
Analyse IRED361 from micromonospora sp. in complex with NADP+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OSN
- Type
- protein
- Length
- 1,739 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase
- UniProt
- A0A1S8Y2S4
- Ligands
- NAP
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 59% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 6-phosphogluconate dehydrogenase | protein | 290 | 59% helix, 12% strand | A0A1S8Y2S4 |
| B | 6-phosphogluconate dehydrogenase | protein | 291 | 58% helix, 12% strand | A0A1S8Y2S4 |
| E, F | 6-phosphogluconate dehydrogenase | protein | 289 | 59% helix, 12% strand | A0A1S8Y2S4 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 966 | 0.85 | 0.86 | 106 | NAP |
| 2 | 387 | 0.75 | 0.85 | 44 | NAP |
| 3 | 393 | 0.75 | 0.85 | 46 | NAP |
| 4 | 59 | 0.74 | 0.99 | 20 | empty |
| 5 | 353 | 0.74 | 0.85 | 44 | NAP |
Interfaces
8 interfaces between chains.
- A–B · 4595 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 4572 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 4013 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 462 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 427 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7OSN · IRED361 from Micromonospora sp. in complex with NADP+ · 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 A0A1S8Y2S4
- Elsewhere: RCSB PDB 7OSN · PDBe 7OSN · UniProt A0A1S8Y2S4
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