MolNFT v1 · #81654 · protein
Crystal structure of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with NADP and preq
3UXV · NADPH-dependent 7-cyano-7-deazaguanine reductase: “Crystal structure of 7-cyano-7-deazaguanine reductase, quef from vibrio cholerae complexed with NADP and preq”. X-ray diffraction, 2 ligands (NAP, GUN), 15 pockets (best…
- PDB
- 3UXV
- Type
- protein
- Length
- 1,026 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
- NAP, GUN
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 27% 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 | 254 | 28% helix, 36% strand | C3LTF1 |
| B, C | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 259 | 26% helix, 36% strand | C3LTF1 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B, C, D
- GUN · Guanine · ligand · 2 copies · chains B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.70 | 0.79 | 53 | empty |
| 2 | 463 | 0.67 | 0.79 | 53 | NAP, GUN |
| 3 | 432 | 0.67 | 0.79 | 55 | GUN, NAP |
| 4 | 219 | 0.62 | 0.82 | 31 | empty |
| 5 | 164 | 0.57 | 0.81 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2211 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2173 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 984 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 221 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 221 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3UXV · 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 3UXV · PDBe 3UXV · UniProt C3LTF1
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