Research workbench
Crystal structure of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with NADP and PREQ0
Analyse Crystal structure of 7-cyano-7-deazaguanine reductase, quef from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UXJ
- 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
- C3LTF1
- Ligands
- PRF, NAP
- Pockets
- 17 · best druggability 0.74
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, 34% strand | C3LTF1 |
| B, C | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 259 | 26% helix, 37% strand | C3LTF1 |
Ligands and binding sites
- PRF · 7-deaza-7-aminomethyl-guanine · ligand · 4 copies · chains A, B, C, D
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.74 | 0.83 | 50 | PRF, NAP |
| 2 | 397 | 0.71 | 0.82 | 52 | PRF, NAP |
| 3 | 50 | 0.67 | 0.97 | 16 | empty |
| 4 | 192 | 0.66 | 0.85 | 23 | empty |
| 5 | 51 | 0.63 | 0.95 | 20 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 2183 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2179 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 1020 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 223 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 213 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 4 covalent (engineered, covalent ligand).
Compared structures
- 3UXJ · 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
- Every structure of UniProt C3LTF1
- Elsewhere: RCSB PDB 3UXJ · PDBe 3UXJ · UniProt C3LTF1
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