Research workbench
Crystal structure of putative alcohol dehedrogenase (YP_298327.1) from ralstonia eutropha JMP134 at 2.10 a resolution
Analyse Crystal structure of putative alcohol dehedrogenase (YP_298327.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JZD
- Type
- protein
- Length
- 1,416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron-containing alcohol dehydrogenase
- UniProt
- Q46TQ1
- Ligands
- NAD, CA, CL
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Iron-containing alcohol dehydrogenase | protein | 354 | 59% helix, 13% strand | Q46TQ1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B, C, D
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C
- P6G · Hexaethylene glycol · additive · 2 copies · chains C, D
- PGE · Triethylene glycol · additive · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.80 | 0.82 | 106 | NAD, CL |
| 2 | 1082 | 0.80 | 0.81 | 96 | CL, NAD |
| 3 | 135 | 0.78 | 0.96 | 45 | empty |
| 4 | 695 | 0.75 | 0.81 | 70 | NAD |
| 5 | 624 | 0.74 | 0.81 | 63 | NAD |
Interfaces
4 interfaces between chains.
- A–B · 1187 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1167 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 331 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3JZD · Crystal structure of Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA… · 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 Q46TQ1
- Elsewhere: RCSB PDB 3JZD · PDBe 3JZD · UniProt Q46TQ1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.