Research workbench
Crystal structure of a computationally designed colicin endonuclease and immunity pair COLEDES3/IMDES3
Analyse Crystal structure of a computationally designed colicin endonuclease and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ERE
- Type
- protein
- Length
- 425 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Colicin; Immunity
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Colicin | protein | 126 | 37% helix, 17% strand | — |
| C | Immunity | protein | 87 | 60% helix, 2% strand | — |
| D | Immunity | protein | 83 | 63% helix, 2% strand | — |
| A | Colicin | protein | 129 | 38% helix, 17% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.38 | 0.74 | 16 | empty |
| 2 | 90 | 0.36 | 0.75 | 21 | empty |
| 3 | 80 | 0.33 | 0.74 | 21 | empty |
| 4 | 84 | 0.31 | 0.73 | 21 | empty |
Interfaces
3 interfaces between chains.
- D–A · 838 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 793 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 308 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6ERE · Crystal structure of a computationally designed colicin endonuclease and immunity pair… · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6ERE · PDBe 6ERE
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