Research workbench
Crystal structure of oxidized T. maritima cobalamin-independent methionine synthase complexed with methyltetrahydrofolate
Analyse Crystal structure of oxidized T. maritima cobalamin-independent methionine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XR2
- Type
- protein
- Length
- 1,443 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
- C2F, MRY, SO4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) | protein | 715 | 44% helix, 14% strand | Q9X112 |
| B | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) | protein | 728 | 43% helix, 14% strand | Q9X112 |
Ligands and binding sites
- C2F · 5-methyl-5,6,7,8-tetrahydrofolic acid · ligand · 2 copies · chains A, B
- 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.78 | 0.86 | 64 | C2F |
| 2 | 597 | 0.78 | 0.84 | 56 | MRY |
| 3 | 705 | 0.78 | 0.83 | 71 | C2F |
| 4 | 50 | 0.69 | 0.97 | 18 | empty |
| 5 | 135 | 0.61 | 0.85 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1285 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1XR2 · Crystal Structure of oxidized T. maritima Cobalamin-Independent Methionine Synthase… · 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 1XR2 · PDBe 1XR2 · UniProt Q9X112
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