MolNFT v1 · #184661 · protein
Dnrk mutant rtcr
7OY1 · Carminomycin 4-O-methyltransferase DNRK,METHYLTRANSFERASE…: “Dnrk mutant rtcr”. X-ray diffraction, 2 ligands (SAH, 3VL), 6 pockets (best druggability 0.85). MolNFT v1 #184661 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7OY1
- Type
- protein
- Length
- 674 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carminomycin 4-O-methyltransferase DNRK,METHYLTRANSFERASE domain-containing…
- EC
- 2.1.1.292, 4.1.1.-
- UniProt
- Q06528, A0A2V2Q0Q4, Q54527, I2N5E8
- Ligands
- SAH, 3VL
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carminomycin 4-O-methyltransferase DNRK,METHYLTRANSFERASE domain-containing PROTEIN,ACLACINOMYCIN 10-hydroxylase rdmb (EC 2.1.1.292, 4.1.1.-) | protein | 334 | 49% helix, 18% strand | Q06528, A0A2V2Q0Q4, Q54527, I2N5E8 |
| B | Carminomycin 4-O-methyltransferase DNRK,METHYLTRANSFERASE domain-containing PROTEIN,ACLACINOMYCIN 10-hydroxylase rdmb (EC 2.1.1.292, 4.1.1.-) | protein | 340 | 47% helix, 18% strand | Q06528, A0A2V2Q0Q4, Q54527, I2N5E8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- 3VL · methyl (1R,2R,4S)-2-ethyl-2,5,7-trihydroxy-6,11-dioxo-4-{[2,3,6-trideoxy-3-(dimethylamino)-alpha-L-lyxo-hexopyranosyl]oxy}-1,2,3,4,6,11-hexahydrotetracene-1-carboxylate · ligand · 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 | 780 | 0.85 | 0.88 | 78 | SAH, 3VL |
| 2 | 824 | 0.85 | 0.87 | 79 | SAH, 3VL |
| 3 | 213 | 0.54 | 0.78 | 35 | empty |
| 4 | 130 | 0.49 | 0.79 | 17 | empty |
| 5 | 144 | 0.43 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 3184 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7OY1 · DnrK mutant RTCR · 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
- Q54527 · AlphaFold monomer V2.0 prediction for aclacinomycin 10-hydroxylase rdmb (Q54527) · a predicted model of the same protein · chain A against A, TM-score 0.93
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
- Every structure of UniProt A0A2V2Q0Q4
- Every structure of UniProt Q54527
- Every structure of UniProt I2N5E8
- Elsewhere: RCSB PDB 7OY1 · PDBe 7OY1 · UniProt Q06528 · UniProt A0A2V2Q0Q4 · UniProt Q54527 · UniProt I2N5E8
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