Research workbench
Crystal structure of the complex of the colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)
Analyse Crystal structure of the complex of the colicin E9 DNase domain with a mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GYK
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E9 immunity protein; Colicin-E9
- EC
- 3.1.21.1
- UniProt
- P13479, P09883
- Ligands
- ZN, PO4
- Pockets
- 2 · best druggability 0.27
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Colicin-E9 immunity protein | protein | 83 | 58% helix, 2% strand | P13479 |
| B | Colicin-E9 (EC 3.1.21.1) | protein | 130 | 42% helix, 17% strand | P09883 |
| F | Colicin-E9 (EC 3.1.21.1) | protein | 132 | 43% 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 | 57 | 0.27 | 0.74 | 13 | PO4 |
| 2 | 53 | 0.26 | 0.74 | 15 | empty |
Interfaces
2 interfaces between chains.
- E–F · 839 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 820 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2GYK · Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity… · 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 F 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 2GYK · PDBe 2GYK · UniProt P13479 · UniProt P09883
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