Research workbench
Following evolutionary paths to high affinity and selectivity protein- protein interactions using COLICIN7 and immunity proteins
Analyse Following evolutionary paths to high affinity and selectivity protein- protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GJN
- Type
- protein
- Length
- 403 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E9 immunity protein; Colicin-E7
- EC
- 3.1.-.-
- UniProt
- P13479, Q47112
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Colicin-E9 immunity protein | protein | 82 | 57% helix, 5% strand | P13479 |
| B | Colicin-E7 (EC 3.1.-.-) | protein | 119 | 41% helix, 15% strand | Q47112 |
| C | Colicin-E7 (EC 3.1.-.-) | protein | 120 | 44% helix, 17% strand | Q47112 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 225 | 0.54 | 0.77 | 32 | empty |
| 2 | 238 | 0.53 | 0.77 | 33 | empty |
| 3 | 212 | 0.53 | 0.78 | 38 | empty |
| 4 | 51 | 0.36 | 0.80 | 15 | empty |
| 5 | 96 | 0.34 | 0.73 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 807 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 806 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 615 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 241 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 229 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3GJN · Following evolutionary paths to high affinity and selectivity protein-protein… · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.96
- Q47112 · AlphaFold monomer V2.0 prediction for colicin-E7 (Q47112) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q47112
- Elsewhere: RCSB PDB 3GJN · PDBe 3GJN · UniProt P13479 · UniProt Q47112
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