Research workbench
Crystal structure of colicin E3 V206C mutant in complex with its immunity protein
Analyse Crystal structure of colicin E3 V206C mutant in complex with its immunity… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B5U
- Type
- protein
- Length
- 1,108 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.-.-
- UniProt
- P00646, P02984
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Colicin E3 (EC 3.1.-.-) | protein | 470 | 39% helix, 24% strand | P00646 |
| B, D | Colicin E3 immunity protein | protein | 84 | 19% helix, 33% strand | P02984 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.69 | 0.76 | 56 | empty |
| 2 | 586 | 0.68 | 0.78 | 44 | empty |
| 3 | 53 | 0.68 | 0.97 | 20 | empty |
| 4 | 164 | 0.64 | 0.85 | 27 | empty |
| 5 | 149 | 0.60 | 0.84 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2118 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2105 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1603 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2B5U · Crystal Structure Of Colicin E3 V206C Mutant 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 0.98
- 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 2B5U · PDBe 2B5U · UniProt P00646 · UniProt P02984
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