Research workbench
Crystal structure of the escherichia COLI colicin E9 DNase domain with its cognate immunity protein IM9
Analyse Crystal structure of the escherichia COLI colicin E9 DNase domain with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BXI
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (colicin E9 immunity protein); Protein (colicin E9)
- UniProt
- P13479, P09883
- Ligands
- NI, PO4
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein (colicin E9 immunity protein) | protein | 83 | 58% helix, 0% strand | P13479 |
| B | Protein (colicin E9) | protein | 131 | 39% helix, 17% strand | P09883 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.38 | 0.78 | 21 | empty |
| 2 | 74 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 1BXI · Crystal structure of the escherichia COLI colicin E9 DNase domain with its cognate… · the same entry in another collection · chain A against A, TM-score 1.00
- P09883 · AlphaFold monomer V2.0 prediction for colicin-E9 (P09883) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P13479 · AlphaFold monomer V2.0 prediction for colicin-E9 immunity protein (P13479) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P13479
- Every structure of UniProt P09883
- Elsewhere: RCSB PDB 1BXI · PDBe 1BXI · UniProt P13479 · UniProt P09883
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