MolNFT v1 · #141657 · protein
Molecular structure of a novel 5,10-methylenetetrahydrofolate dehydrogenase from the silkworm, bombyx mori
5ZF1: “Molecular structure of a novel 5,10-methylenetetrahydrofolate dehydrogenase from the silkworm, bombyx mori”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.65). MolNFT v1 #141657 on GenesisL1: 3D structure…
- PDB
- 5ZF1
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5,10-methylenetetrahydrofolate dehydrogenase
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5,10-methylenetetrahydrofolate dehydrogenase | protein | 288 | 43% helix, 16% strand | — |
| B | 5,10-methylenetetrahydrofolate dehydrogenase | protein | 290 | 43% helix, 15% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.65 | 0.78 | 44 | empty |
| 2 | 360 | 0.61 | 0.77 | 37 | empty |
| 3 | 176 | 0.57 | 0.81 | 43 | SO4 |
| 4 | 120 | 0.39 | 0.74 | 29 | EDO |
| 5 | 87 | 0.36 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1647 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5ZF1 · Molecular structure of a novel 5,10-methylenetetrahydrofolate dehydrogenase from 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
- Elsewhere: RCSB PDB 5ZF1 · PDBe 5ZF1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.