Research workbench
Crystal structures of nuclease-COLE7 complexed with octamer DNA
Analyse Crystal structures of nuclease-COLE7 complexed with octamer DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PT3
- Type
- protein + DNA
- Length
- 304 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-gcgatcgc-3'; Colicin E7
- EC
- 3.1.-.-
- UniProt
- Q47112
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D, G, H, E, F | 5'-gcgatcgc-3' | dna | 8 | — | — |
| A, B | Colicin E7 (EC 3.1.-.-) | protein | 128 | 40% helix, 17% strand | Q47112 |
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.63 | 0.79 | 30 | empty |
| 2 | 305 | 0.60 | 0.78 | 30 | empty |
| 3 | 218 | 0.49 | 0.76 | 30 | empty |
| 4 | 165 | 0.44 | 0.75 | 26 | empty |
| 5 | 98 | 0.43 | 0.79 | 13 | empty |
Interfaces
19 interfaces between chains.
- C–A · 467 Ų buried · 11 hydrogen bonds · protein-nucleic
- E–B · 457 Ų buried · 10 hydrogen bonds · protein-nucleic
- E–F · 368 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- C–D · 367 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- G–H · 365 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
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 1PT3 · PDBe 1PT3 · UniProt Q47112
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