Research workbench
Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-bp duplex DNA
Analyse Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FBD
- Type
- protein + DNA
- Length
- 335 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E7; 5'-D(*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DAP*DTP*DCP*DGP*DAP*D…
- EC
- 3.1.-.-
- UniProt
- Q47112
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin-E7 (EC 3.1.-.-) | protein | 132 | 36% helix, 17% strand | Q47112 |
| B, C, E, F | 5'-D(*DGP*DGP*DAP*DAP*DTP*DTP*DCP*DGP*DAP*DTP*DCP*DGP*DAP*D AP*DTP*DTP*DCP*DC)-3' | dna | 18 | — | — |
| D | Colicin-E7 (EC 3.1.-.-) | protein | 131 | 36% helix, 17% strand | Q47112 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 266 | 0.60 | 0.79 | 31 | empty |
| 2 | 253 | 0.58 | 0.79 | 29 | empty |
| 3 | 127 | 0.49 | 0.80 | 17 | empty |
| 4 | 114 | 0.46 | 0.79 | 16 | empty |
| 5 | 81 | 0.40 | 0.79 | 16 | empty |
Interfaces
10 interfaces between chains.
- E–F · 805 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- B–C · 801 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- D–E · 624 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 595 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 443 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 3FBD · Crystal structure of the nuclease domain of COLE7(D493Q mutant) in complex with an 18-BP… · the same entry in another collection · chain F against F, TM-score 1.00
- Q47112 · AlphaFold monomer V2.0 prediction for colicin-E7 (Q47112) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q47112
- Elsewhere: RCSB PDB 3FBD · PDBe 3FBD · UniProt Q47112
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