MolNFT v1 · #22518 · protein
Crystal structure of cobalamin-independent methionine synthase from T. maritima
1T7L · 5-methyltetrahydropteroyltriglutamate--homocysteine…: “Crystal structure of cobalamin-independent methionine synthase from T. maritima”. X-ray diffraction, 2 ligands (MRY, SO4), 17 pockets (best druggability 0.80). MolNFT v1 #22518…
- PDB
- 1T7L
- Type
- protein
- Length
- 1,465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
- EC
- 2.1.1.14
- UniProt
- Q9X112
- Ligands
- MRY, SO4
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) | protein | 734 | 44% helix, 14% strand | Q9X112 |
| B | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) | protein | 731 | 44% helix, 14% strand | Q9X112 |
Ligands and binding sites
- MRY · Meso-erythritol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 850 | 0.80 | 0.83 | 71 | MRY |
| 2 | 467 | 0.73 | 0.82 | 36 | empty |
| 3 | 630 | 0.73 | 0.80 | 63 | empty |
| 4 | 546 | 0.71 | 0.80 | 40 | empty |
| 5 | 324 | 0.70 | 0.83 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1282 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1T7L · Crystal Structure of Cobalamin-Independent Methionine Synthase from T. maritima · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X112 · AlphaFold monomer V2.0 prediction for 5-methyltetrahydropteroyltriglutamate--homocysteine… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X112
- Elsewhere: RCSB PDB 1T7L · PDBe 1T7L · UniProt Q9X112
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