Research workbench
Oxidized precursor form of glucose-fructose oxidoreductase from zymomonas mobilis complexed with glycerol
Analyse Oxidized precursor form of glucose-fructose oxidoreductase from zymomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H6D
- Type
- protein
- Length
- 4,579 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Precursor form of glucose-fructose oxidoreductase
- EC
- 1.1.99.28
- UniProt
- P75002
- Ligands
- NDP
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Precursor form of glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 383 | 37% helix, 22% strand | P75002 |
| B, F, G, H, J, L | Precursor form of glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 381 | 37% helix, 22% strand | P75002 |
| C, D, E, I, K | Precursor form of glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 382 | 37% helix, 22% strand | P75002 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains A, C, B, D, E, G, F, H, I, K, J, L
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 870 | 0.88 | 0.90 | 97 | empty |
| 2 | 865 | 0.87 | 0.90 | 87 | empty |
| 3 | 865 | 0.87 | 0.90 | 93 | empty |
| 4 | 1013 | 0.85 | 0.86 | 81 | empty |
| 5 | 1049 | 0.85 | 0.86 | 80 | empty |
Interfaces
24 interfaces between chains.
- I–K · 3422 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 3415 Ų buried · 31 hydrogen bonds · protein-protein
- E–G · 3407 Ų buried · 32 hydrogen bonds · protein-protein
- J–L · 3401 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 3396 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 1H6D · Oxidized Precursor Form of Glucose-Fructose Oxidoreductase from Zymomonas mobilis… · 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 P75002
- Elsewhere: RCSB PDB 1H6D · PDBe 1H6D · UniProt P75002
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