Research workbench
Crystal structure of 3-quinuclidinone reductase from agrobacterium tumefaciens
Analyse Crystal structure of 3-quinuclidinone reductase from agrobacterium tumefaciens in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WDS
- Type
- protein
- Length
- 1,028 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-dependent quinuclidinone reductase
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, C | NADH-dependent quinuclidinone reductase | protein | 257 | 52% helix, 14% strand | — |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
- ACY · Acetic acid · additive · 4 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.85 | 0.86 | 117 | NAD |
| 2 | 1152 | 0.85 | 0.85 | 111 | NAD |
| 3 | 242 | 0.83 | 0.96 | 32 | empty |
| 4 | 62 | 0.39 | 0.80 | 19 | empty |
| 5 | 85 | 0.39 | 0.77 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1751 Ų buried · 29 hydrogen bonds · protein-protein
- D–C · 1716 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1588 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1557 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 88 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3WDS · Crystal structure of 3-quinuclidi reductase from Agrobacterium tumefaciens · 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 3WDS · PDBe 3WDS
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