Research workbench
Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed conformation
Analyse Crystal structure of the cobalamin-independent methionine synthase enzyme in a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QQU
- Type
- protein
- Length
- 766 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
- EC
- 2.1.1.14
- UniProt
- P82610
- Ligands
- HCS, 39S, ZN, PO4
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) | protein | 766 | 45% helix, 14% strand | P82610 |
Ligands and binding sites
- HCS · 2-amino-4-mercapto-butyric acid · ligand · chains A
- 39S · N-[4-({[(6S)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-gamma-glutamyl-L-gamma-glutamyl-L-glutamic acid · ligand · chains A
- ZN · Zinc ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.79 | 0.84 | 91 | HCS, 39S |
| 2 | 97 | 0.78 | 0.98 | 21 | empty |
| 3 | 722 | 0.73 | 0.79 | 64 | empty |
| 4 | 480 | 0.67 | 0.79 | 59 | empty |
| 5 | 172 | 0.60 | 0.82 | 21 | empty |
Compared structures
- 4QQU · Crystal structure of the cobalamin-independent methionine synthase enzyme in a closed… · the same entry in another collection · chain A against A, TM-score 1.00
- P82610 · AlphaFold monomer V2.0 prediction for 5-methyltetrahydropteroyltriglutamate--homocysteine… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P82610
- Elsewhere: RCSB PDB 4QQU · PDBe 4QQU · UniProt P82610
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