Research workbench
Structure of epoxyqueuosine reductase from streptococcus thermophilus.
Analyse Structure of epoxyqueuosine reductase from streptococcus thermophilus. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6S
- Type
- protein
- Length
- 1,847 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxyqueuosine reductase
- UniProt
- A0A0F7K4Z9
- Ligands
- SF4, B12
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Epoxyqueuosine reductase | protein | 370 | 45% helix, 10% strand | A0A0F7K4Z9 |
| C | Epoxyqueuosine reductase | protein | 367 | 45% helix, 10% strand | A0A0F7K4Z9 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 10 copies · chains A, B, C, D, E
- B12 · Cobalamin · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.84 | 0.86 | 63 | SF4, B12 |
| 2 | 844 | 0.84 | 0.86 | 61 | SF4, B12 |
| 3 | 1074 | 0.82 | 0.83 | 63 | SF4, B12 |
| 4 | 1102 | 0.82 | 0.83 | 67 | SF4, B12 |
| 5 | 1123 | 0.82 | 0.83 | 74 | SF4, B12 |
Interfaces
7 interfaces between chains.
- C–E · 545 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 110 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 60 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D6S · Structure of epoxyqueuosine reductase from Streptococcus thermophilus. · 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 A0A0F7K4Z9
- Elsewhere: RCSB PDB 5D6S · PDBe 5D6S · UniProt A0A0F7K4Z9
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