MolNFT v1 · #186625 · protein
Mannitol-2-dehydrogenase bound to NADH from aspergillus fumigatus
7RK5 · Mannitol 2-dehydrogenase: “Mannitol-2-dehydrogenase bound to NADH from aspergillus fumigatus”. X-ray diffraction, 1 ligand (NAI), 8 pockets (best druggability 0.83). MolNFT v1 #186625 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RK5
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannitol 2-dehydrogenase
- EC
- 1.1.1.67
- UniProt
- Q4WQY4
- Ligands
- NAI
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Mannitol 2-dehydrogenase (EC 1.1.1.67) | protein | 501 | 52% helix, 13% strand | Q4WQY4 |
| A | Mannitol 2-dehydrogenase (EC 1.1.1.67) | protein | 489 | 53% helix, 13% strand | Q4WQY4 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.83 | 0.85 | 112 | NAI |
| 2 | 234 | 0.61 | 0.81 | 40 | empty |
| 3 | 154 | 0.51 | 0.79 | 27 | empty |
| 4 | 68 | 0.46 | 0.83 | 21 | NAI |
| 5 | 56 | 0.42 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 600 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7RK5 · Mannitol-2-dehydrogenase bound to NADH from Aspergillus fumigatus · the same entry in another collection · chain B against B, TM-score 1.00
- Q4WQY4 · AlphaFold monomer V2.0 prediction for mannitol 2-dehydrogenase (Q4WQY4) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q4WQY4
- Elsewhere: RCSB PDB 7RK5 · PDBe 7RK5 · UniProt Q4WQY4
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