Research workbench
Reduced homo sapiens betaine-homocysteine S-methyltransferase in complex with S-(delta-carboxybutyl)-L-homocysteine
Analyse Reduced 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
- 1LT8
- Type
- protein
- Length
- 688 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
- CBH, ZN
- Pockets
- 7 · best druggability 0.81
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 | 348 | 47% helix, 11% strand | Q93088 |
| B | Betaine-homocysteine methyltransferase (EC 2.1.1.5) | protein | 340 | 45% helix, 12% strand | Q93088 |
Ligands and binding sites
- CBH · S-(D-carboxybutyl)-L-homocysteine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 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
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.81 | 0.98 | 29 | empty |
| 2 | 137 | 0.80 | 0.97 | 34 | CBH |
| 3 | 132 | 0.79 | 0.97 | 28 | CBH |
| 4 | 205 | 0.60 | 0.81 | 25 | empty |
| 5 | 200 | 0.56 | 0.79 | 33 | CIT |
Interfaces
1 interface between chains.
- A–B · 3585 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 1LT8 · Reduced Homo sapiens Betaine-Homocysteine S-Methyltransferase in Complex with… · 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 B 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 Q93088
- Elsewhere: RCSB PDB 1LT8 · PDBe 1LT8 · UniProt Q93088
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