MolNFT v1 · #27230 · protein
Crystal structure of T. maritima cobalamin-independent methionine synthase complexed with ZN2+ and homocysteine
1XDJ · 5-methyltetrahydropteroyltriglutamate--homocysteine…: “Crystal structure of T. maritima cobalamin-independent methionine synthase complexed with ZN2+ and…”. X-ray diffraction, 4 ligands (HCS, MRY, ZN), 17 pockets (best druggability…
- PDB
- 1XDJ
- Type
- protein
- Length
- 1,434 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
- HCS, MRY, ZN, SO4
- Pockets
- 17 · best druggability 0.79
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 | 722 | 44% helix, 14% strand | Q9X112 |
| B | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) | protein | 712 | 43% helix, 15% strand | Q9X112 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · 2 copies · chains A, B
- MRY · Meso-erythritol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.79 | 0.84 | 58 | MRY |
| 2 | 402 | 0.74 | 0.84 | 44 | empty |
| 3 | 370 | 0.72 | 0.83 | 43 | empty |
| 4 | 234 | 0.67 | 0.84 | 28 | HCS |
| 5 | 239 | 0.65 | 0.83 | 31 | HCS |
Interfaces
1 interface between chains.
- A–B · 1274 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 modified (engineered).
Compared structures
- 1XDJ · Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with… · 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 1XDJ · PDBe 1XDJ · UniProt Q9X112
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