Research workbench
Crystal structure of the intact mtase from vibrio vulnificus YJ016 in complex with the DNA-mimicking ocr protein and the S-adenosyl-L- homocysteine (sah)
Analyse Crystal structure of the intact mtase from vibrio vulnificus YJ016 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EEW
- Type
- protein
- Length
- 720 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type I restriction-modification system methyltransferase subunit; Overcome classical…
- UniProt
- Q7MJG0, P03775
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type I restriction-modification system methyltransferase subunit | protein | 610 | 40% helix, 12% strand | Q7MJG0 |
| B | Overcome classical restriction GP0.3 | protein | 110 | 65% helix, 0% strand | P03775 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.69 | 0.94 | 19 | empty |
| 2 | 287 | 0.69 | 0.83 | 43 | SAH |
| 3 | 146 | 0.46 | 0.76 | 30 | empty |
| 4 | 68 | 0.32 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1112 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7EEW · Crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the… · the same entry in another collection · 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 Q7MJG0
- Every structure of UniProt P03775
- Elsewhere: RCSB PDB 7EEW · PDBe 7EEW · UniProt Q7MJG0 · UniProt P03775
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