Research workbench
Binding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the functional geometry of the catalytic site
Analyse Binding of two substrate analogue molecules to dihydroflavonol 4-reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BXX
- Type
- protein
- Length
- 1,944 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroflavonol 4-reductase
- EC
- 1.1.1.219
- UniProt
- P93799
- Ligands
- QUE, NAP
- Pockets
- 19 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Dihydroflavonol 4-reductase (EC 1.1.1.219) | protein | 324 | 44% helix, 15% strand | P93799 |
Ligands and binding sites
- QUE · 3,5,7,3',4'-pentahydroxyflavone · ligand · 9 copies · chains A, D, B, C, F, E
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.88 | 0.89 | 122 | NAP, QUE |
| 2 | 560 | 0.83 | 0.89 | 74 | NAP |
| 3 | 502 | 0.82 | 0.89 | 64 | NAP, QUE |
| 4 | 416 | 0.81 | 0.89 | 46 | NAP, QUE |
| 5 | 240 | 0.81 | 0.93 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1567 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1492 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1397 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 446 Ų buried · 1 hydrogen bond · protein-protein
- B–F · 403 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3BXX · Binding of two substrate analogue molecules to dihydroflavonol 4-reductase alters the… · 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 P93799
- Elsewhere: RCSB PDB 3BXX · PDBe 3BXX · UniProt P93799
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