Research workbench
Structure of the mitomycin 7-O-methyltransferase mmcr
Analyse Structure of the mitomycin 7-O-methyltransferase mmcr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GWZ
- Type
- protein
- Length
- 1,356 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mmcr
- UniProt
- Q9X5T6
- Ligands
- SAH, CA
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, C, B | Mmcr | protein | 339 | 53% helix, 16% strand | Q9X5T6 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, D, C, B
- CA · Calcium ion · metal · 4 copies · chains A, D
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, D, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.81 | 0.84 | 78 | MPD, SAH |
| 2 | 699 | 0.80 | 0.84 | 63 | MPD, SAH |
| 3 | 1062 | 0.80 | 0.82 | 87 | MPD, SAH |
| 4 | 978 | 0.80 | 0.82 | 86 | MPD, SAH |
| 5 | 258 | 0.60 | 0.80 | 37 | empty |
Interfaces
3 interfaces between chains.
- D–C · 3365 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3306 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 468 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3GWZ · Structure of the Mitomycin 7-O-methyltransferase MmcR · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X5T6 · AlphaFold monomer V2.0 prediction for mitomycin biosynthesis 6-O-methyltransferase… · a predicted model of the same protein · chain C 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 Q9X5T6
- Elsewhere: RCSB PDB 3GWZ · PDBe 3GWZ · UniProt Q9X5T6
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