Research workbench
Crystal structure of the 2,6-dihydroxy-pseudo-oxynicotine hydrolase.
Analyse Crystal structure of the 2,6-dihydroxy-pseudo-oxynicotine hydrolase. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2JBW
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,6-dihydroxy-pseudo-oxynicotine hydrolase
- EC
- 3.7.1.-
- UniProt
- Q93NG6
- Ligands
- NA
- Pockets
- 14 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,6-dihydroxy-pseudo-oxynicotine hydrolase (EC 3.7.1.-) | protein | 359 | 49% helix, 16% strand | Q93NG6 |
| B | 2,6-dihydroxy-pseudo-oxynicotine hydrolase (EC 3.7.1.-) | protein | 360 | 48% helix, 16% strand | Q93NG6 |
| C | 2,6-dihydroxy-pseudo-oxynicotine hydrolase (EC 3.7.1.-) | protein | 351 | 50% helix, 17% strand | Q93NG6 |
| D | 2,6-dihydroxy-pseudo-oxynicotine hydrolase (EC 3.7.1.-) | protein | 359 | 49% helix, 16% strand | Q93NG6 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, 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 | 1119 | 0.82 | 0.83 | 96 | empty |
| 2 | 1184 | 0.81 | 0.82 | 81 | empty |
| 3 | 479 | 0.78 | 0.85 | 53 | empty |
| 4 | 446 | 0.74 | 0.84 | 39 | empty |
| 5 | 166 | 0.70 | 0.89 | 28 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1168 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1074 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 338 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 modified (engineered).
Compared structures
- 2JBW · Crystal Structure of the 2,6-dihydroxy-pseudo-oxynicotine Hydrolase. · the same entry in another collection · chain D against D, TM-score 1.00
- Q93NG6 · AlphaFold monomer V2.0 prediction for 2,6-dihydropseudooxynicotine hydrolase (Q93NG6) · a predicted model of the same protein · chain B 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 Q93NG6
- Elsewhere: RCSB PDB 2JBW · PDBe 2JBW · UniProt Q93NG6
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