MolNFT v1 · #154816 · protein
Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scfv
6KN9 · Interleukin-18 receptor accessory protein: “Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic…”. X-ray diffraction, 1 ligand (NAG), 19 pockets (best druggability 0.72).…
- 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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