MolNFT v1 · #99561 · protein
Mutant structure of methyltransferase from streptomyces hygroscopicus
4M72 · Methyltransferase mppj: “Mutant structure of methyltransferase from streptomyces hygroscopicus”. X-ray diffraction, 5 ligands (SAH, M72, HF2), 6 pockets (best druggability 0.75). MolNFT v1 #99561 on GenesisL1: 3D structure, binding…
- PDB
- 4M72
- Type
- protein
- Length
- 666 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, M72, HF2, CA, FE
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Methyltransferase mppj (EC 2.1.1.-) | protein | 333 | 54% helix, 17% strand | Q643C8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- M72 · (2R,3R)-2-hydroxy-3-methoxy-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 · 8 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
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 | 73 | 0.75 | 0.99 | 19 | empty |
| 2 | 646 | 0.73 | 0.80 | 57 | SAH, M72, FE |
| 3 | 604 | 0.72 | 0.80 | 53 | SAH, M72, FE |
| 4 | 124 | 0.46 | 0.78 | 17 | empty |
| 5 | 108 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3284 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4M72 · 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 B 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 4M72 · PDBe 4M72 · UniProt Q643C8
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