MolNFT v1 · #78177 · protein
Crystal structure of the R262L mutant of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with PREQ0
3S19 · NADPH-dependent 7-cyano-7-deazaguanine reductase: “Crystal structure of the R262L mutant of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae…”. X-ray diffraction, 1 ligand (PRF), 16 pockets (best druggability 0.73).…
- PDB
- 3S19
- Type
- protein
- Length
- 1,040 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH-dependent 7-cyano-7-deazaguanine reductase
- EC
- 1.7.1.13
- UniProt
- Q9KTK0
- Ligands
- PRF
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 261 | 26% helix, 36% strand | Q9KTK0 |
| B, C | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 259 | 26% helix, 36% strand | Q9KTK0 |
Ligands and binding sites
- PRF · 7-deaza-7-aminomethyl-guanine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 462 | 0.73 | 0.82 | 54 | PRF |
| 2 | 417 | 0.73 | 0.83 | 53 | PRF |
| 3 | 52 | 0.64 | 0.95 | 19 | GOL |
| 4 | 489 | 0.63 | 0.76 | 43 | empty |
| 5 | 216 | 0.60 | 0.81 | 28 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2180 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2147 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 990 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 217 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 3S19 · Crystal Structure of the R262L mutant of 7-cyano-7-deazaguanine reductase, QueF from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KTK0 · AlphaFold monomer V2.0 prediction for NADPH-dependent 7-cyano-7-deazaguanine reductase… · a predicted model of the same protein · chain B 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 Q9KTK0
- Elsewhere: RCSB PDB 3S19 · PDBe 3S19 · UniProt Q9KTK0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.