MolNFT v1 · #4267 · protein
Crystal structure of a monoclinic form of dihydropteridine reductase from rat liver
1DIR: “Crystal structure of a monoclinic form of dihydropteridine reductase from rat liver”. X-ray diffraction, 1 ligand (NAD), 8 pockets (best druggability 0.68). MolNFT v1 #4267 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1DIR
- Type
- protein
- Length
- 944 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteridine reductase
- EC
- 1.6.99.7
- UniProt
- P11348
- Ligands
- NAD
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Dihydropteridine reductase (EC 1.6.99.7) | protein | 236 | 40% helix, 24% strand | P11348 |
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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 445 | 0.68 | 0.79 | 47 | NAD |
| 2 | 411 | 0.68 | 0.80 | 47 | NAD |
| 3 | 425 | 0.68 | 0.80 | 49 | NAD |
| 4 | 420 | 0.68 | 0.80 | 48 | NAD |
| 5 | 503 | 0.67 | 0.78 | 56 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1870 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1817 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1DIR · Crystal structure of a monoclinic form of dihydropteridine reductase from rat liver · the same entry in another collection · chain D against D, TM-score 1.00
- P11348 · AlphaFold monomer V2.0 prediction for dihydropteridine reductase (P11348) · 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 P11348
- Elsewhere: RCSB PDB 1DIR · PDBe 1DIR · UniProt P11348
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