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Mutant structure of methyltransferase from streptomyces hygroscopicus
Analyse Mutant structure of methyltransferase from streptomyces hygroscopicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M74
- Type
- protein
- Length
- 671 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase mppj
- EC
- 2.1.1.-
- UniProt
- Q643C8
- Ligands
- SAH, M74, HF2, CA, FE
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase mppj (EC 2.1.1.-) | protein | 333 | 53% helix, 17% strand | Q643C8 |
| B | Methyltransferase mppj (EC 2.1.1.-) | protein | 338 | 51% helix, 16% strand | Q643C8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- M74 · (2S,3R)-2,3-dihydroxy-3-phenylpropanoic acid · ligand · 2 copies · chains A, B
- HF2 · (2R)-2-hydroxy-3-phenylpropanoic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.77 | 0.99 | 21 | empty |
| 2 | 706 | 0.75 | 0.81 | 60 | SAH, M74, FE |
| 3 | 718 | 0.75 | 0.80 | 60 | SAH, M74, FE |
| 4 | 225 | 0.53 | 0.77 | 29 | empty |
| 5 | 110 | 0.47 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3388 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4M74 · Mutant structure of methyltransferase from Streptomyces hygroscopicus · the same entry in another collection · chain B against B, TM-score 1.00
- Q643C8 · AlphaFold monomer V2.0 prediction for phenylpyruvate C(3)-methyltransferase (Q643C8) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q643C8
- Elsewhere: RCSB PDB 4M74 · PDBe 4M74 · UniProt Q643C8
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