Research workbench
Oxidized homo sapiens betaine-homocysteine S-methyltransferase in complex with four SM(III) ions
Analyse Oxidized homo sapiens betaine-homocysteine S-methyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LT7
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine-homocysteine methyltransferase
- EC
- 2.1.1.5
- UniProt
- Q93088
- Ligands
- SM
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Betaine-homocysteine methyltransferase (EC 2.1.1.5) | protein | 305 | 47% helix, 12% strand | Q93088 |
| B | Betaine-homocysteine methyltransferase (EC 2.1.1.5) | protein | 315 | 46% helix, 12% strand | Q93088 |
Ligands and binding sites
- SM · Samarium (III) ion · metal · 4 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.78 | 0.80 | 110 | empty |
| 2 | 244 | 0.56 | 0.78 | 29 | SM, CIT |
| 3 | 161 | 0.56 | 0.81 | 31 | SM, CIT |
| 4 | 64 | 0.33 | 0.76 | 14 | empty |
| 5 | 64 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2689 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1LT7 · Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four… · the same entry in another collection · chain A against A, TM-score 1.00
- Q93088 · AlphaFold monomer V2.0 prediction for betaine--homocysteine S-methyltransferase 1 (Q93088) · 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 Q93088
- Elsewhere: RCSB PDB 1LT7 · PDBe 1LT7 · UniProt Q93088
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.