Research workbench
Miab in the complex with 5'-deoxyadenosine, methionine and RNA
Analyse Miab in the complex with 5'-deoxyadenosine, methionine and RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MJX
- Type
- protein + RNA
- Length
- 909 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase; RNA…
- EC
- 2.8.4.3
- UniProt
- A0A174NUT3
- Ligands
- F3S, SF4, 5AD, MET, NA
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (EC 2.8.4.3) | protein | 442 | 38% helix, 24% strand | A0A174NUT3 |
| B | TRNA-2-methylthio-N(6)-dimethylallyladenosine synthase (EC 2.8.4.3) | protein | 441 | 38% helix, 24% strand | A0A174NUT3 |
| D, M | RNA (5'-R(*GP*GP*AP*CP*UP*GP*AP*AP*(MIA)P*AP*UP*CP*C)-3') | rna | 13 | — | — |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, M, B, D
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 5AD · 5'-deoxyadenosine · ligand · 2 copies · chains A, M, B, D
- MET · Methionine · ligand · 2 copies · chains A, M, B, D
- NA · Sodium ion · metal · 3 copies · chains A, B, M
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.85 | 0.96 | 39 | F3S, SF4, 5AD, MET |
| 2 | 267 | 0.84 | 0.96 | 40 | F3S, SF4, 5AD, MET |
| 3 | 409 | 0.79 | 0.89 | 59 | NA |
| 4 | 526 | 0.78 | 0.85 | 70 | empty |
| 5 | 75 | 0.35 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–D · 1374 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–M · 1369 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 588 Ų buried · 4 hydrogen bonds · protein-protein
- D–M · 150 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 7MJX · MiaB in the complex with 5'-deoxyadenosine, methionine 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 7MJX · PDBe 7MJX · UniProt A0A174NUT3
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