Research workbench
Mannitol dehydrogenase from agaricus bisporus
Analyse Mannitol dehydrogenase from agaricus bisporus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H5Q
- Type
- protein
- Length
- 3,120 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent mannitol dehydrogenase
- EC
- 1.1.1.138
- UniProt
- O93868
- Ligands
- NAP, NI
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | NADP-dependent mannitol dehydrogenase (EC 1.1.1.138) | protein | 260 | 50% helix, 20% strand | O93868 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NI · Nickel (II) ion · metal · 6 copies · chains A, C, B, D, E, G, F, H, I, K, J, 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 | 1028 | 0.87 | 0.89 | 156 | NAP |
| 2 | 989 | 0.85 | 0.86 | 72 | NI |
| 3 | 977 | 0.85 | 0.86 | 70 | NI |
| 4 | 1009 | 0.85 | 0.86 | 74 | NI |
| 5 | 1081 | 0.79 | 0.80 | 99 | empty |
Interfaces
26 interfaces between chains.
- F–G · 1759 Ų buried · 17 hydrogen bonds · protein-protein
- J–K · 1757 Ų buried · 21 hydrogen bonds · protein-protein
- E–H · 1753 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1746 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1745 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 1H5Q · Mannitol dehydrogenase from Agaricus bisporus · the same entry in another collection · chain L against L, 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 O93868
- Elsewhere: RCSB PDB 1H5Q · PDBe 1H5Q · UniProt O93868
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