Research workbench
Structure of the borneol dehydrogenases of salvia rosmarinus with NAD+
Analyse Structure of the borneol dehydrogenases of salvia rosmarinus with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZYZ
- Type
- protein
- Length
- 1,035 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Borneol dehydrogenase from salvia rosmarinus
- Ligands
- NAD, PXN, CL
- Pockets
- 17 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Borneol dehydrogenase from salvia rosmarinus | protein | 259 | 51% helix, 16% strand | — |
| B | Borneol dehydrogenase from salvia rosmarinus | protein | 258 | 52% helix, 16% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- PXN · (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol · ligand · 2 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.86 | 0.87 | 66 | CL |
| 2 | 407 | 0.72 | 0.82 | 44 | NAD |
| 3 | 486 | 0.69 | 0.80 | 49 | NAD |
| 4 | 396 | 0.66 | 0.79 | 43 | NAD |
| 5 | 409 | 0.65 | 0.78 | 43 | NAD |
Interfaces
6 interfaces between chains.
- A–D · 1619 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1572 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1539 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1519 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 923 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ZYZ · Structure of the borneol dehydrogenases of Salvia rosmarinus 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 6ZYZ · PDBe 6ZYZ
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