Research workbench
Crystal structure of methyltransferase from streptomyces hygroscopicus complexed with S-adenosyl-L-homocysteine and methylphenylpyruvic acid
Analyse Crystal 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
- 4KIB
- Type
- protein
- Length
- 668 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase mppj
- UniProt
- Q643C8
- Ligands
- SAH, 56D, HF2, CA, FE
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase mppj | protein | 333 | 55% helix, 17% strand | Q643C8 |
| B | Methyltransferase mppj | protein | 335 | 54% helix, 16% strand | Q643C8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 56D · (3R)-2-oxo-3-phenylbutanoic acid · ligand · 2 copies · chains A, B
- HF2 · (2R)-2-hydroxy-3-phenylpropanoic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 5 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 | 536 | 0.77 | 0.84 | 60 | SAH, 56D, FE |
| 2 | 538 | 0.77 | 0.84 | 52 | SAH, 56D, FE |
| 3 | 74 | 0.76 | 0.99 | 18 | empty |
| 4 | 132 | 0.46 | 0.77 | 16 | empty |
| 5 | 103 | 0.45 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3203 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified, 2 covalent (engineered, covalent ligand).
Compared structures
- 4KIB · Crystal structure of methyltransferase from Streptomyces hygroscopicus complexed with… · the same entry in another collection · chain A against A, 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 0.96
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 4KIB · PDBe 4KIB · UniProt Q643C8
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