Research workbench
Alcohol dehydrogenase from arthrobacter sp. ts-15 in complex with NAD+
Analyse Alcohol dehydrogenase from arthrobacter sp. ts-15 in complex with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QHE
- Type
- protein
- Length
- 1,555 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alcohol dehydrogenase
- EC
- 1.1.1.1
- Ligands
- NAD, NA
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 261 | 49% helix, 17% strand | — |
| B, E | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 258 | 49% helix, 16% strand | — |
| C, F | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 259 | 49% helix, 17% strand | — |
| D | Alcohol dehydrogenase (EC 1.1.1.1) | protein | 260 | 49% helix, 17% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 5 copies · chains A, B, C, D, F
- NA · Sodium ion · metal · 4 copies · chains A, D, B, C, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 819 | 0.85 | 0.87 | 52 | empty |
| 2 | 955 | 0.83 | 0.84 | 122 | empty |
| 3 | 519 | 0.76 | 0.83 | 48 | NAD |
| 4 | 503 | 0.76 | 0.83 | 54 | NAD |
| 5 | 502 | 0.75 | 0.83 | 51 | NAD |
Interfaces
8 interfaces between chains.
- C–D · 1697 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 1671 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 1652 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 1629 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1623 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6QHE · Alcohol Dehydrogenase from Arthrobacter sp. TS-15 in complex with NAD+ · 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
- Elsewhere: RCSB PDB 6QHE · PDBe 6QHE
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