MolNFT v1 · #64522 · protein
Crystal structure of trans-aconitate 3-methyltransferase from yeast
3G5T: “Crystal structure of trans-aconitate 3-methyltransferase from yeast”. X-ray diffraction, 2 ligands (SAH, T8N), 3 pockets (best druggability 0.74). MolNFT v1 #64522 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3G5T
- Type
- protein
- Length
- 299 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trans-aconitate 3-methyltransferase
- EC
- 2.1.1.145
- UniProt
- P32643
- Ligands
- SAH, T8N
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trans-aconitate 3-methyltransferase (EC 2.1.1.145) | protein | 299 | 40% helix, 22% strand | P32643 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- T8N · (2E)-2-(2-methoxy-2-oxoethyl)but-2-enedioic acid · ligand · chains A
- EDO · 1,2-ethanediol · additive · 8 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.74 | 0.89 | 52 | EDO, SAH, T8N |
| 2 | 53 | 0.32 | 0.77 | 13 | empty |
| 3 | 58 | 0.29 | 0.74 | 13 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3G5T · Crystal structure of trans-aconitate 3-methyltransferase from yeast · the same entry in another collection · chain A against A, TM-score 1.00
- P32643 · AlphaFold monomer V2.0 prediction for trans-aconitate 3-methyltransferase (P32643) · 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 P32643
- Elsewhere: RCSB PDB 3G5T · PDBe 3G5T · UniProt P32643
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