MolNFT v1 · #134597 · protein + RNA
Structure of epoxyqueuosine reductase from bacillus subtilis with the ASP134 catalytic loop swung out of the active site.
5T8Y: “Structure of epoxyqueuosine reductase from bacillus subtilis with the ASP134 catalytic loop swung out of the…”. X-ray diffraction, 3 ligands (SF4, B12, PO4), 8 pockets (best druggability 0.81). MolNFT v1 #134597 on GenesisL1: 3D…
- PDB
- 5T8Y
- Type
- protein + RNA
- Length
- 751 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxyqueuosine reductase; RNA (5'- R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3…
- EC
- 1.17.99.6
- UniProt
- P97030
- Ligands
- SF4, B12, PO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 374 | 46% helix, 10% strand | P97030 |
| B | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 372 | 44% helix, 11% strand | P97030 |
| X | RNA (5'- R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') | rna | 5 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.81 | 0.82 | 72 | SF4, B12, PO4 |
| 2 | 1144 | 0.80 | 0.81 | 70 | SF4, B12, PO4 |
| 3 | 102 | 0.47 | 0.81 | 18 | empty |
| 4 | 155 | 0.47 | 0.77 | 27 | empty |
| 5 | 151 | 0.45 | 0.76 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–B · 886 Ų buried · 13 hydrogen bonds · protein-protein
- B–X · 363 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5T8Y · Structure of epoxyqueuosine reductase from Bacillus subtilis with the Asp134 catalytic… · the same entry in another collection · chain A against A, TM-score 1.00
- P97030 · AlphaFold monomer V2.0 prediction for epoxyqueuosine reductase (P97030) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P97030
- Elsewhere: RCSB PDB 5T8Y · PDBe 5T8Y · UniProt P97030
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