Research workbench
Crystal structure of yldv 14L il-18 binding protein in complex with human il-18
Analyse Crystal structure of yldv 14L il-18 binding protein in complex with human il-18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EKX
- Type
- protein
- Length
- 498 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 14L protein; Interleukin-18
- UniProt
- Q9DHU8, Q14116
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 14L protein | protein | 100 | 13% helix, 49% strand | Q9DHU8 |
| B | Interleukin-18 | protein | 142 | 2% helix, 54% strand | Q14116 |
| D | Interleukin-18 | protein | 155 | 6% helix, 53% strand | Q14116 |
| A | 14L protein | protein | 101 | 13% helix, 47% strand | Q9DHU8 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.45 | 0.77 | 19 | empty |
| 2 | 86 | 0.41 | 0.78 | 18 | empty |
| 3 | 68 | 0.39 | 0.79 | 18 | empty |
| 4 | 91 | 0.37 | 0.76 | 18 | empty |
| 5 | 72 | 0.34 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1029 Ų buried · 11 hydrogen bonds · protein-protein
- B–A · 954 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 765 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4EKX · Crystal Structure of YLDV 14L IL-18 Binding Protein in Complex with Human IL-18 · the same entry in another collection · chain C against C, TM-score 1.00
- Q14116 · AlphaFold monomer V2.0 prediction for interleukin-18 (Q14116) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9DHU8
- Every structure of UniProt Q14116
- Elsewhere: RCSB PDB 4EKX · PDBe 4EKX · UniProt Q9DHU8 · UniProt Q14116
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