MolNFT v1 · #19051 · protein
Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (CD2+ complex, se-met)
1Q85 · 5-methyltetrahydrofolate S-homocysteine methyltransferase: “Cobalamin-dependent methionine synthase (1-566) from thermotoga maritima (CD2+ complex, se-met)”. X-ray diffraction, 1 ligand (CD), 10 pockets (best druggability 0.61).…
- PDB
- 1Q85
- Type
- protein
- Length
- 1,109 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
- CD
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methyltetrahydrofolate S-homocysteine methyltransferase (EC 2.1.1.13) | protein | 559 | 46% helix, 14% strand | Q9WYA5 |
| B | 5-methyltetrahydrofolate S-homocysteine methyltransferase (EC 2.1.1.13) | protein | 550 | 47% helix, 13% strand | Q9WYA5 |
Ligands and binding sites
- CD · Cadmium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.61 | 0.81 | 32 | empty |
| 2 | 211 | 0.59 | 0.81 | 29 | empty |
| 3 | 341 | 0.55 | 0.75 | 35 | empty |
| 4 | 323 | 0.55 | 0.75 | 39 | empty |
| 5 | 137 | 0.51 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1107 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 1Q85 · Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima (Cd2+ complex… · 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 1Q85 · PDBe 1Q85 · UniProt Q9WYA5
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