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
- 3C1T
- Type
- protein
- Length
- 1,292 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroflavonol 4-reductase
- EC
- 1.1.1.219
- UniProt
- P93799
- Ligands
- MYC, NAP
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroflavonol 4-reductase (EC 1.1.1.219) | protein | 320 | 43% helix, 17% strand | P93799 |
| B | Dihydroflavonol 4-reductase (EC 1.1.1.219) | protein | 326 | 44% helix, 16% strand | P93799 |
| C | Dihydroflavonol 4-reductase (EC 1.1.1.219) | protein | 325 | 43% helix, 16% strand | P93799 |
| D | Dihydroflavonol 4-reductase (EC 1.1.1.219) | protein | 321 | 45% helix, 16% strand | P93799 |
Ligands and binding sites
- MYC · 3,5,7-trihydroxy-2-(3,4,5-trihydroxyphenyl)-4H-chromen-4-one · ligand · 8 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.85 | 0.85 | 82 | NAP, MYC |
| 2 | 878 | 0.81 | 0.83 | 70 | NAP, MYC |
| 3 | 869 | 0.79 | 0.81 | 66 | NAP, MYC |
| 4 | 837 | 0.78 | 0.81 | 66 | NAP, MYC |
| 5 | 162 | 0.45 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–D · 489 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 467 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 458 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 24 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3C1T · 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 3C1T · PDBe 3C1T · UniProt P93799
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