MolNFT v1 · #142414 · protein
Levoglucosan dehydrogenase, complex with NADH and levoglucosan
6A3I · Putative dehydrogenase: “Levoglucosan dehydrogenase, complex with NADH and levoglucosan”. X-ray diffraction, 2 ligands (NAI, 4PW), 14 pockets (best druggability 0.87). MolNFT v1 #142414 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6A3I
- Type
- protein
- Length
- 1,475 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydrogenase
- UniProt
- F0M433
- Ligands
- NAI, 4PW
- Pockets
- 14 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dehydrogenase | protein | 372 | 35% helix, 25% strand | F0M433 |
| B | Putative dehydrogenase | protein | 370 | 38% helix, 25% strand | F0M433 |
| C | Putative dehydrogenase | protein | 367 | 37% helix, 25% strand | F0M433 |
| D | Putative dehydrogenase | protein | 366 | 36% helix, 25% strand | F0M433 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 3 copies · chains A, B, C
- 4PW · Levoglucosan · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.87 | 0.88 | 115 | empty |
| 2 | 419 | 0.69 | 0.81 | 69 | NAI |
| 3 | 352 | 0.66 | 0.80 | 55 | NAI |
| 4 | 255 | 0.66 | 0.83 | 41 | 4PW, NAI |
| 5 | 330 | 0.64 | 0.79 | 44 | 4PW |
Interfaces
6 interfaces between chains.
- A–C · 1832 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 1792 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1614 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1601 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 702 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6A3I · Levoglucosan dehydrogenase, complex with NADH and levoglucosan · 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 6A3I · PDBe 6A3I · UniProt F0M433
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