Research workbench
Crystal structure of dihydropteridine reductase from dictyostelium discoideum
Analyse Crystal structure of dihydropteridine reductase from dictyostelium discoideum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ORF
- Type
- protein
- Length
- 920 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteridine reductase
- EC
- 1.5.1.34
- UniProt
- Q86A17
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydropteridine reductase (EC 1.5.1.34) | protein | 230 | 42% helix, 24% strand | Q86A17 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.83 | 0.84 | 84 | empty |
| 2 | 380 | 0.69 | 0.81 | 39 | NAD |
| 3 | 374 | 0.65 | 0.79 | 39 | NAD |
| 4 | 341 | 0.62 | 0.79 | 38 | NAD |
| 5 | 301 | 0.60 | 0.78 | 35 | NAD |
Interfaces
5 interfaces between chains.
- C–D · 1790 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1755 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 231 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 211 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3ORF · Crystal Structure of Dihydropteridine Reductase from Dictyostelium discoideum · the same entry in another collection · chain D against D, TM-score 1.00
- Q86A17 · AlphaFold monomer V2.0 prediction for dihydropteridine reductase (Q86A17) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q86A17
- Elsewhere: RCSB PDB 3ORF · PDBe 3ORF · UniProt Q86A17
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