MolNFT v1 · #59142 · protein
Crystal structure of putative 7-cyano-7-deazaguanine reductase quef from vibrio cholerae O1 biovar eltor
3BP1 · NADPH-dependent 7-cyano-7-deazaguanine reductase: “Crystal structure of putative 7-cyano-7-deazaguanine reductase quef from vibrio cholerae O1 biovar eltor”. X-ray diffraction, 4 ligands (GUN, POP, MG), 14 pockets (best druggability…
- PDB
- 3BP1
- Type
- protein
- Length
- 1,019 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
- A6Y463
- Ligands
- GUN, POP, MG, PO4
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 255 | 27% helix, 36% strand | A6Y463 |
| B, C | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 254 | 26% helix, 36% strand | A6Y463 |
| D | NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.13) | protein | 256 | 27% helix, 36% strand | A6Y463 |
Ligands and binding sites
- GUN · Guanine · ligand · 4 copies · chains A, B, C, D
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 368 | 0.65 | 0.80 | 56 | GUN, POP |
| 2 | 238 | 0.64 | 0.82 | 36 | empty |
| 3 | 470 | 0.63 | 0.76 | 35 | empty |
| 4 | 213 | 0.62 | 0.82 | 22 | empty |
| 5 | 188 | 0.61 | 0.83 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2179 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2147 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 991 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 211 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3BP1 · Crystal structure of putative 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 A6Y463
- Elsewhere: RCSB PDB 3BP1 · PDBe 3BP1 · UniProt A6Y463
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