MolNFT v1 · #93692 · protein
Structural insights into the reduction mechanism of saccharomyces cerevisia riboflavin biosynthesis reductase RIB7
4HA9 · 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate…: “Structural insights into the reduction mechanism of saccharomyces cerevisia riboflavin biosynthesis reductase…”. X-ray diffraction, 1 ligand (NDP), 6 pockets (best…
- PDB
- 4HA9
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase
- EC
- 1.1.1.302
- UniProt
- P33312
- Ligands
- NDP
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase (EC 1.1.1.302) | protein | 219 | 23% helix, 27% strand | P33312 |
| B | 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase (EC 1.1.1.302) | protein | 204 | 21% helix, 27% strand | P33312 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.61 | 0.76 | 43 | empty |
| 2 | 52 | 0.50 | 0.87 | 15 | empty |
| 3 | 91 | 0.38 | 0.76 | 15 | empty |
| 4 | 98 | 0.38 | 0.76 | 21 | NDP |
| 5 | 103 | 0.35 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1337 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4HA9 · Structural insights into the reduction mechanism of Saccharomyces cerevisia Riboflavin… · the same entry in another collection · chain A against A, TM-score 1.00
- P33312 · AlphaFold monomer V2.0 prediction for 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P33312
- Elsewhere: RCSB PDB 4HA9 · PDBe 4HA9 · UniProt P33312
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