Research workbench
Crystal structure of an alcohol dehydrogenase from elizabethkingia anophelis NUHP1
Analyse Crystal structure of an alcohol dehydrogenase from elizabethkingia anophelis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7L
- Type
- protein
- Length
- 4,102 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- UniProt
- A0A077EGR8
- Ligands
- NAD, ZN, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H, K | Alcohol dehydrogenase | protein | 342 | 30% helix, 29% strand | A0A077EGR8 |
| C | Alcohol dehydrogenase | protein | 344 | 30% helix, 29% strand | A0A077EGR8 |
| D, J | Alcohol dehydrogenase | protein | 343 | 30% helix, 29% strand | A0A077EGR8 |
| E, G, L | Alcohol dehydrogenase | protein | 340 | 31% helix, 29% strand | A0A077EGR8 |
| F | Alcohol dehydrogenase | protein | 343 | 30% helix, 29% strand | A0A077EGR8 |
| I | Alcohol dehydrogenase | protein | 341 | 31% helix, 29% strand | A0A077EGR8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 12 copies · chains A, D, B, C, E, H, F, G, I, L, J, K
- ZN · Zinc ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- EDO · 1,2-ethanediol · additive · 90 copies · chains A, C, D, B, J, G, F, E, H, I, K, 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 | 1169 | 0.83 | 0.84 | 144 | EDO |
| 2 | 1056 | 0.82 | 0.84 | 136 | EDO |
| 3 | 383 | 0.80 | 0.89 | 58 | NAD |
| 4 | 463 | 0.77 | 0.85 | 77 | NAD, EDO |
| 5 | 386 | 0.77 | 0.87 | 56 | EDO, NAD |
Interfaces
24 interfaces between chains.
- A–D · 1899 Ų buried · 25 hydrogen bonds · protein-protein
- I–L · 1895 Ų buried · 31 hydrogen bonds · protein-protein
- J–K · 1890 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 1879 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 1876 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6N7L · Crystal structure of an alcohol dehydrogenase from Elizabethkingia anophelis NUHP1 · 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 A0A077EGR8
- Elsewhere: RCSB PDB 6N7L · PDBe 6N7L · UniProt A0A077EGR8
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