Research workbench
Crystal structure of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae
Analyse Crystal structure of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJ4
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 7-cyano-7-deazaguanine reductase quef
- Ligands
- CL, SO4
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 7-cyano-7-deazaguanine reductase quef | protein | 259 | 30% helix, 32% strand | — |
| B | 7-cyano-7-deazaguanine reductase quef | protein | 255 | 26% helix, 34% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · chains A
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 | 379 | 0.61 | 0.77 | 57 | GOL, SO4 |
| 2 | 50 | 0.50 | 0.88 | 14 | empty |
| 3 | 130 | 0.45 | 0.77 | 25 | empty |
| 4 | 52 | 0.44 | 0.84 | 16 | empty |
| 5 | 105 | 0.43 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 2220 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3RJ4 · Crystal Structure of 7-cyano-7-deazaguanine Reductase, QueF from Vibrio cholerae · 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
- Elsewhere: RCSB PDB 3RJ4 · PDBe 3RJ4
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