MolNFT v1 · #182204 · protein + RNA
Miab in the complex with S-adenosyl-L-homocysteine and RNA
7MJY · TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase: “Miab in the complex with S-adenosyl-L-homocysteine and RNA”. X-ray diffraction, 4 ligands (F3S, SF4, SAH), 1 pocket (best druggability 0.81). MolNFT v1 #182204 on GenesisL1…
- PDB
- 7MJY
- Type
- protein + RNA
- Length
- 453 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; RNA (5'-R(P*UP*AP*UP*UP*C)-3')
- EC
- 2.8.4.3
- UniProt
- A0A174NUT3
- Ligands
- F3S, SF4, SAH, CL
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (EC 2.8.4.3) | protein | 448 | 38% helix, 23% strand | A0A174NUT3 |
| M | RNA (5'-R(P*UP*AP*UP*UP*C)-3') | rna | 5 | — | — |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A
- PGE · Triethylene glycol · additive · 3 copies · chains A, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 807 | 0.81 | 0.84 | 84 | PGE, F3S, SF4, SAH |
Interfaces
1 interface between chains.
- A–M · 603 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 7MJY · MiaB in the complex with s-adenosyl-L-homocysteine and RNA · 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 A0A174NUT3
- Elsewhere: RCSB PDB 7MJY · PDBe 7MJY · UniProt A0A174NUT3
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