MolNFT v1 · #115999 · protein + RNA
Crystal structure of epoxyqueuosine reductase with a tRNA-tyr epoxyqueuosine-modified tRNA stem loop
5D0B: “Crystal structure of epoxyqueuosine reductase with a tRNA-tyr epoxyqueuosine-modified tRNA stem loop”. X-ray diffraction, 3 ligands (SF4, B12, PO4), 9 pockets (best druggability 0.84). MolNFT v1 #115999 on GenesisL1: 3D structure…
- PDB
- 5D0B
- Type
- protein + RNA
- Length
- 768 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxyqueuosine reductase; RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)…
- EC
- 1.17.99.6
- UniProt
- P97030
- Ligands
- SF4, B12, PO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 376 | 47% helix, 11% strand | P97030 |
| B | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 375 | 47% helix, 11% strand | P97030 |
| F | RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B) P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') | rna | 17 | — | — |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B
- B12 · Cobalamin · ligand · 2 copies · chains A, B, F
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.84 | 0.85 | 76 | SF4, B12 |
| 2 | 1059 | 0.83 | 0.84 | 69 | SF4, B12 |
| 3 | 528 | 0.66 | 0.77 | 65 | empty |
| 4 | 234 | 0.64 | 0.83 | 25 | GOL |
| 5 | 90 | 0.39 | 0.77 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–F · 800 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 734 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5D0B · Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified… · 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 5D0B · PDBe 5D0B · UniProt P97030
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