Research workbench
Crystal structure of carminomycin-4-O-methyltransferase (dnrk) in complex with S-adenosyl-L-homocystein (sah) and 4-methoxy-E-rhodomycin T (M-et)
Analyse Crystal structure of carminomycin-4-O-methyltransferase (dnrk) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TW2
- Type
- protein
- Length
- 688 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carminomycin 4-O-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q06528
- Ligands
- SAH, ERT
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carminomycin 4-O-methyltransferase (EC 2.1.1.-) | protein | 338 | 47% helix, 17% strand | Q06528 |
| B | Carminomycin 4-O-methyltransferase (EC 2.1.1.-) | protein | 350 | 46% helix, 17% strand | Q06528 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- ERT · Methyl (4R)-2-ethyl-2,5,12-trihydroxy-7-methoxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-beta-D-ribo-hexopyranosyl]oxy}-1H,2H,3H,4H,6H,11H-tetracene-1-carboxylate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.86 | 0.91 | 66 | SAH, ERT |
| 2 | 1117 | 0.82 | 0.83 | 90 | SAH, ERT |
| 3 | 73 | 0.41 | 0.80 | 15 | empty |
| 4 | 101 | 0.39 | 0.76 | 19 | empty |
| 5 | 92 | 0.33 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 3726 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 1TW2 · Crystal structure of Carminomycin-4-O-methyltransferase (DnrK) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q06528 · AlphaFold monomer V2.0 prediction for carminomycin 4-O-methyltransferase dnrk (Q06528) · 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 Q06528
- Elsewhere: RCSB PDB 1TW2 · PDBe 1TW2 · UniProt Q06528
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