MolNFT v1 · #142412 · protein
Levoglucosan dehydrogenase, complex with NADH
6A3G · Putative dehydrogenase: “Levoglucosan dehydrogenase, complex with NADH”. X-ray diffraction, 1 ligand (NAI), 15 pockets (best druggability 0.87). MolNFT v1 #142412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6A3G
- Type
- protein
- Length
- 1,489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydrogenase
- UniProt
- F0M433
- Ligands
- NAI
- Pockets
- 15 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dehydrogenase | protein | 372 | 37% helix, 25% strand | F0M433 |
| B | Putative dehydrogenase | protein | 372 | 38% helix, 26% strand | F0M433 |
| C | Putative dehydrogenase | protein | 374 | 38% helix, 25% strand | F0M433 |
| D | Putative dehydrogenase | protein | 371 | 37% helix, 26% strand | F0M433 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.87 | 0.88 | 106 | empty |
| 2 | 263 | 0.68 | 0.84 | 42 | NAI |
| 3 | 244 | 0.67 | 0.84 | 41 | NAI |
| 4 | 293 | 0.66 | 0.82 | 44 | NAI |
| 5 | 253 | 0.66 | 0.83 | 41 | NAI |
Interfaces
6 interfaces between chains.
- A–B · 1848 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1812 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1623 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1608 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6A3G · Levoglucosan dehydrogenase, complex with NADH · 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 6A3G · PDBe 6A3G · UniProt F0M433
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