MolNFT v1 · #106312 · protein
Crystal structure of mtmc in complex with sah and tdp-4-keto-D-olivose
4RVH · D-mycarose 3-C-methyltransferase: “Crystal structure of mtmc in complex with sah and tdp-4-keto-D-olivose”. X-ray diffraction, 3 ligands (SAH, 3YN, ZN), 2 pockets (best druggability 0.84). MolNFT v1 #106312 on GenesisL1: 3D…
- PDB
- 4RVH
- Type
- protein
- Length
- 418 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-mycarose 3-C-methyltransferase
- UniProt
- Q194Q4
- Ligands
- SAH, 3YN, ZN
- Pockets
- 2 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-mycarose 3-C-methyltransferase | protein | 418 | 37% helix, 22% strand | Q194Q4 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- 3YN · [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,4R,6R)-4-hydroxy-6-methyl-5-oxotetrahydro-2H-pyran-2-yl dihydrogen diphosphate · ligand · chains A
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.84 | 0.88 | 88 | SAH, 3YN |
| 2 | 70 | 0.29 | 0.73 | 22 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4RVH · Crystal structure of MtmC in complex with SAH and TDP-4-keto-D-olivose · 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 Q194Q4
- Elsewhere: RCSB PDB 4RVH · PDBe 4RVH · UniProt Q194Q4
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