Research workbench
Crystal structure of selenomethionine-labeled epoxyqueuosine reductase
Analyse Crystal structure of selenomethionine-labeled epoxyqueuosine reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D08
- Type
- protein
- Length
- 759 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxyqueuosine reductase
- EC
- 1.17.99.6
- UniProt
- P97030
- Ligands
- SF4, B12, PO4, CL
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 384 | 47% helix, 11% strand | P97030 |
| B | Epoxyqueuosine reductase (EC 1.17.99.6) | protein | 375 | 47% helix, 12% strand | P97030 |
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 · 2 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1010 | 0.84 | 0.85 | 64 | SF4, B12, GOL |
| 2 | 1019 | 0.83 | 0.84 | 65 | SF4, B12, GOL |
| 3 | 101 | 0.37 | 0.75 | 19 | empty |
| 4 | 100 | 0.36 | 0.75 | 18 | empty |
| 5 | 64 | 0.26 | 0.72 | 11 | empty |
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 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 5D08 · PDBe 5D08 · UniProt P97030
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