Research workbench
Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7 ångströms)
Analyse Crystal structure of colicin E9 DNase domain with its cognate immunity protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EMV
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunity protein IM9; Colicin E9
- EC
- 3.1.21.1
- UniProt
- P13479, P09883
- Ligands
- PO4
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunity protein IM9 | protein | 83 | 58% helix, 0% strand | P13479 |
| B | Colicin E9 (EC 3.1.21.1) | protein | 131 | 41% helix, 17% strand | P09883 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.29 | 0.73 | 17 | PO4 |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 1EMV · Crystal structure of colicin E9 DNase domain with its cognate immunity protein IM9 (1.7… · 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 1EMV · PDBe 1EMV · UniProt P13479 · UniProt P09883
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