Research workbench
Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scfv
Analyse Crystal structure of human interleukin 18 receptor beta extracellular domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KN9
- Type
- protein
- Length
- 1,320 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-18 receptor accessory protein; Scfv
- UniProt
- O95256
- Ligands
- NAG
- Pockets
- 19 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-18 receptor accessory protein | protein | 260 | 2% helix, 51% strand | O95256 |
| B | Interleukin-18 receptor accessory protein | protein | 224 | 4% helix, 47% strand | O95256 |
| C | Interleukin-18 receptor accessory protein | protein | 261 | 2% helix, 49% strand | O95256 |
| D | Scfv | protein | 220 | 3% helix, 48% strand | — |
| E | Scfv | protein | 134 | 0% helix, 37% strand | — |
| F | Scfv | protein | 221 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 680 | 0.72 | 0.79 | 74 | empty |
| 2 | 664 | 0.68 | 0.76 | 83 | empty |
| 3 | 457 | 0.59 | 0.74 | 61 | empty |
| 4 | 292 | 0.59 | 0.78 | 42 | empty |
| 5 | 361 | 0.56 | 0.75 | 37 | empty |
Interfaces
7 interfaces between chains.
- C–F · 1152 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1035 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 894 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 143 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6KN9 · Crystal structure of human interleukin 18 receptor beta extracellular domain in complex… · the same entry in another collection · chain F against F, TM-score 1.00
- O95256 · AlphaFold monomer V2.0 prediction for interleukin-18 receptor accessory protein (O95256) · a predicted model of the same protein · chain A against A, TM-score 0.56
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 O95256
- Elsewhere: RCSB PDB 6KN9 · PDBe 6KN9 · UniProt O95256
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