Research workbench
Structure of epoxyqueuosine reductase from bacillus subtilis with the ASP134 catalytic loop swung out of the active site.
Analyse Structure of epoxyqueuosine reductase from bacillus subtilis with the ASP134… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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