Research workbench
Crystal structure of IM3 in complex with Y52A mutant of E3RNASE
Analyse Crystal structure of IM3 in complex with Y52A mutant of E3RNASE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UDM
- Type
- protein
- Length
- 180 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin-E3 immunity protein; Colicin-E3
- UniProt
- P02984, P00646
- Ligands
- CA, CL
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Colicin-E3 immunity protein | protein | 84 | 17% helix, 33% strand | P02984 |
| B | Colicin-E3 | protein | 96 | 13% helix, 33% strand | P00646 |
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 | 52 | 0.49 | 0.86 | 15 | empty |
| 2 | 78 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1360 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4UDM · Crystal structure of Im3 in complex with Y52A mutant of E3RNase · 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 B 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 A 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 P02984
- Every structure of UniProt P00646
- Elsewhere: RCSB PDB 4UDM · PDBe 4UDM · UniProt P02984 · UniProt P00646
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