MolNFT v1 · #137444 · protein
Methionine synthase folate-binding domain from thermus thermophilus HB8 native
5VOP · 5-methyltetrahydrofolate homocysteine S-methyltransferase: “Methionine synthase folate-binding domain from thermus thermophilus HB8 native”. X-ray diffraction, 2 ligands (C2F, NA), 3 pockets (best druggability 0.58). MolNFT v1…
- PDB
- 5VOP
- Type
- protein
- Length
- 564 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydrofolate homocysteine S-methyltransferase
- UniProt
- Q5SKM5
- Ligands
- C2F, NA
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methyltetrahydrofolate homocysteine S-methyltransferase | protein | 282 | 51% helix, 17% strand | Q5SKM5 |
Ligands and binding sites
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.58 | 0.76 | 43 | C2F |
| 2 | 337 | 0.57 | 0.76 | 32 | C2F |
| 3 | 51 | 0.33 | 0.78 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 946 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5VOP · Methionine synthase folate-binding domain from Thermus thermophilus HB8 native · 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 Q5SKM5
- Elsewhere: RCSB PDB 5VOP · PDBe 5VOP · UniProt Q5SKM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.