Research workbench
Crystal structure of quec from bacillus subtilis: an enzyme involved in PREQ1 biosynthesis
Analyse Crystal structure of quec from bacillus subtilis: an enzyme involved in PREQ1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BL5
- Type
- protein
- Length
- 1,178 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Queuosine biosynthesis protein quec
- EC
- 3.5.-.-
- UniProt
- O31675
- Ligands
- ZN, MG, PO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Queuosine biosynthesis protein quec (EC 3.5.-.-) | protein | 195 | 51% helix, 12% strand | O31675 |
| E, F | Queuosine biosynthesis protein quec (EC 3.5.-.-) | protein | 199 | 50% helix, 13% strand | O31675 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 748 | 0.73 | 0.78 | 51 | empty |
| 2 | 774 | 0.73 | 0.78 | 51 | empty |
| 3 | 785 | 0.72 | 0.78 | 48 | MG, PO4 |
| 4 | 676 | 0.72 | 0.78 | 48 | empty |
| 5 | 610 | 0.65 | 0.75 | 47 | MG, PO4 |
Interfaces
8 interfaces between chains.
- A–D · 1662 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1652 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 608 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 580 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 577 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3BL5 · Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis · the same entry in another collection · chain F against F, TM-score 1.00
- O31675 · AlphaFold monomer V2.0 prediction for 7-cyano-7-deazaguanine synthase (O31675) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 O31675
- Elsewhere: RCSB PDB 3BL5 · PDBe 3BL5 · UniProt O31675
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