MolNFT v1 · #19064 · protein
Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (CD2+, hcy, methyltetrahydrofolate complex)
1Q8J · 5-methyltetrahydrofolate S-homocysteine methyltransferase: “Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (CD2+, hcy, methyltetrahydrofolate…”. X-ray diffraction, 3 ligands (HCS, C2F, CD), 8 pockets (best…
- PDB
- 1Q8J
- Type
- protein
- Length
- 1,097 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydrofolate S-homocysteine methyltransferase
- EC
- 2.1.1.13
- UniProt
- Q9WYA5
- Ligands
- HCS, C2F, CD
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methyltetrahydrofolate S-homocysteine methyltransferase (EC 2.1.1.13) | protein | 559 | 47% helix, 15% strand | Q9WYA5 |
| B | 5-methyltetrahydrofolate S-homocysteine methyltransferase (EC 2.1.1.13) | protein | 538 | 49% helix, 14% strand | Q9WYA5 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 2 copies · chains A, B
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.57 | 0.80 | 39 | CD, HCS |
| 2 | 156 | 0.56 | 0.81 | 28 | HCS |
| 3 | 295 | 0.53 | 0.75 | 34 | C2F |
| 4 | 128 | 0.49 | 0.80 | 16 | empty |
| 5 | 135 | 0.49 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1105 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1Q8J · Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+, Hcy… · 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 Q9WYA5
- Elsewhere: RCSB PDB 1Q8J · PDBe 1Q8J · UniProt Q9WYA5
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