MolNFT v1 · #142415 · protein
Levoglucosan dehydrogenase, complex with NADH and L-sorbose
6A3J · Putative dehydrogenase: “Levoglucosan dehydrogenase, complex with NADH and L-sorbose”. X-ray diffraction, 2 ligands (SOE, NAI), 15 pockets (best druggability 0.88). MolNFT v1 #142415 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6A3J
- Type
- protein
- Length
- 1,497 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydrogenase
- UniProt
- F0M433
- Ligands
- SOE, NAI
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Putative dehydrogenase | protein | 373 | 36% helix, 25% strand | F0M433 |
| C | Putative dehydrogenase | protein | 378 | 36% helix, 25% strand | F0M433 |
Ligands and binding sites
- SOE · alpha-L-sorbopyranose · ligand · 4 copies · chains A, D, B, C
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.88 | 0.89 | 133 | empty |
| 2 | 346 | 0.71 | 0.84 | 47 | MES, SOE, NAI |
| 3 | 243 | 0.65 | 0.83 | 37 | MES, SOE, NAI |
| 4 | 183 | 0.65 | 0.85 | 39 | SOE, NAI |
| 5 | 238 | 0.64 | 0.82 | 41 | SOE, NAI |
Interfaces
6 interfaces between chains.
- A–D · 1842 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1825 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1616 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1614 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 695 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6A3J · Levoglucosan dehydrogenase, complex with NADH and L-sorbose · 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 F0M433
- Elsewhere: RCSB PDB 6A3J · PDBe 6A3J · UniProt F0M433
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