MolNFT v1 · #137443 · protein
Methionine synthase folate-binding domain with methyltetrahydrofolate from thermus thermophilus HB8
5VOO · 5-methyltetrahydrofolate homocysteine S-methyltransferase: “Methionine synthase folate-binding domain with methyltetrahydrofolate from thermus thermophilus HB8”. X-ray diffraction, 3 ligands (C2F, NA, CL), 15 pockets (best…
- PDB
- 5VOO
- Type
- protein
- Length
- 1,687 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydrofolate homocysteine S-methyltransferase
- UniProt
- Q5SKM5
- Ligands
- C2F, NA, CL
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methyltetrahydrofolate homocysteine S-methyltransferase | protein | 282 | 52% helix, 17% strand | Q5SKM5 |
| C | 5-methyltetrahydrofolate homocysteine S-methyltransferase | protein | 282 | 50% helix, 16% strand | Q5SKM5 |
| D, F | 5-methyltetrahydrofolate homocysteine S-methyltransferase | protein | 280 | 51% helix, 17% strand | Q5SKM5 |
| E | 5-methyltetrahydrofolate homocysteine S-methyltransferase | protein | 281 | 51% helix, 16% strand | Q5SKM5 |
Ligands and binding sites
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 6 copies · chains A, C, B, D, E, F
- NA · Sodium ion · metal · 6 copies · chains A, C, E, B, D, F
- CL · Chloride ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.86 | 0.87 | 89 | C2F, NA |
| 2 | 629 | 0.74 | 0.80 | 73 | empty |
| 3 | 605 | 0.66 | 0.76 | 57 | NA, CL |
| 4 | 396 | 0.60 | 0.76 | 46 | C2F, NA, PEG |
| 5 | 96 | 0.60 | 0.87 | 21 | empty |
Interfaces
8 interfaces between chains.
- A–C · 1135 Ų buried · 24 hydrogen bonds · protein-protein
- A–E · 959 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 955 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 955 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 430 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5VOO · Methionine synthase folate-binding domain with methyltetrahydrofolate from Thermus… · 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 5VOO · PDBe 5VOO · UniProt Q5SKM5
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