Research workbench
Toxin receptor complex
Analyse Toxin receptor complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IMT
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intermedilysin; CD59 glycoprotein
- UniProt
- Q9LCB8, P13987
- Ligands
- ZN, CU, SO4
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Intermedilysin | protein | 460 | 17% helix, 42% strand | Q9LCB8 |
| D | CD59 glycoprotein | protein | 77 | 17% helix, 32% strand | P13987 |
Ligands and binding sites
- ZN · Zinc ion · metal · 7 copies · chains A, D
- CU · Copper (II) ion · metal · 2 copies · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A, D
- PGE · Triethylene glycol · additive · chains A
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 | 83 | 0.67 | 0.92 | 22 | empty |
| 2 | 131 | 0.61 | 0.86 | 24 | empty |
| 3 | 187 | 0.55 | 0.80 | 36 | empty |
| 4 | 142 | 0.48 | 0.78 | 24 | empty |
| 5 | 77 | 0.43 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–D · 699 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
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 Q9LCB8
- Every structure of UniProt P13987
- Elsewhere: RCSB PDB 5IMT · PDBe 5IMT · UniProt Q9LCB8 · UniProt P13987
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