Research workbench
Crystal structure of colicin E3 in complex with its immunity protein
Analyse Crystal structure of colicin E3 in complex with its immunity protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JCH
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin E3; Colicin E3 immunity protein
- EC
- 3.1.21.-
- UniProt
- P00646, P02984
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Colicin E3 (EC 3.1.21.-) | protein | 468 | 34% helix, 13% strand | P00646 |
| B, D | Colicin E3 immunity protein | protein | 84 | 19% helix, 33% strand | P02984 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, C
- GOL · Glycerol · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.70 | 0.79 | 42 | empty |
| 2 | 54 | 0.70 | 0.97 | 17 | empty |
| 3 | 571 | 0.69 | 0.78 | 47 | empty |
| 4 | 232 | 0.67 | 0.84 | 61 | empty |
| 5 | 97 | 0.66 | 0.91 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2132 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2132 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1635 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1JCH · Crystal Structure of Colicin E3 in Complex with its Immunity Protein · the same entry in another collection · chain A against A, TM-score 1.00
- P00646 · AlphaFold monomer V2.0 prediction for colicin-E3 (P00646) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P02984 · AlphaFold monomer V2.0 prediction for colicin-E3 immunity protein (P02984) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P00646
- Every structure of UniProt P02984
- Elsewhere: RCSB PDB 1JCH · PDBe 1JCH · UniProt P00646 · UniProt P02984
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.