Research workbench
Crystal structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with PREQ1
Analyse Crystal structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, quef… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RZP
- Type
- protein
- Length
- 1,024 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 0.72
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 254 | 27% helix, 34% strand | Q9KTK0 |
| B | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 258 | 26% helix, 32% strand | Q9KTK0 |
| C | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 257 | 27% helix, 33% strand | Q9KTK0 |
| D | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 255 | 29% helix, 32% strand | Q9KTK0 |
Ligands and binding sites
- PRF · 7-deaza-7-aminomethyl-guanine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.72 | 0.97 | 26 | empty |
| 2 | 513 | 0.69 | 0.79 | 56 | empty |
| 3 | 208 | 0.66 | 0.85 | 38 | empty |
| 4 | 352 | 0.66 | 0.80 | 53 | PRF, GOL |
| 5 | 348 | 0.61 | 0.78 | 50 | PRF, GOL |
Interfaces
5 interfaces between chains.
- A–B · 2221 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2203 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 879 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 220 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3RZP · Crystal Structure of the C194A mutant of 7-cyano-7-deazaguanine reductase, QueF from… · the same entry in another collection · chain D against D, 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 C 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 3RZP · PDBe 3RZP · UniProt Q9KTK0
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