MolNFT v1 · #137226 · protein
Il-33/ST2/IL-1RACP ternary complex structure
5VI4 · Interleukin-33: “Il-33/ST2/IL-1RACP ternary complex structure”. X-ray diffraction, 1 ligand (NAG), 15 pockets (best druggability 0.81). MolNFT v1 #137226 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VI4
- Type
- protein
- Length
- 1,405 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-33; Interleukin-1 receptor-like 1; Interleukin-1 receptor accessory protein
- UniProt
- Q8BVZ5, P14719, Q61730
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Interleukin-33 | protein | 146 | 5% helix, 51% strand | Q8BVZ5 |
| B | Interleukin-1 receptor-like 1 | protein | 242 | 5% helix, 55% strand | P14719 |
| C | Interleukin-1 receptor accessory protein | protein | 305 | 6% helix, 48% strand | Q61730 |
| E | Interleukin-1 receptor-like 1 | protein | 260 | 6% helix, 58% strand | P14719 |
| F | Interleukin-1 receptor accessory protein | protein | 306 | 8% helix, 46% strand | Q61730 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 861 | 0.81 | 0.83 | 98 | empty |
| 2 | 1090 | 0.80 | 0.82 | 115 | empty |
| 3 | 450 | 0.69 | 0.80 | 55 | empty |
| 4 | 315 | 0.68 | 0.82 | 42 | empty |
| 5 | 663 | 0.66 | 0.75 | 60 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1761 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1736 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1407 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1296 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 574 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5VI4 · IL-33/ST2/IL-1RAcP ternary complex structure · the same entry in another collection · chain F against F, TM-score 1.00
- Q8BVZ5 · AlphaFold monomer V2.0 prediction for interleukin-33 (Q8BVZ5) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q61730 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor accessory protein (Q61730) · a predicted model of the same protein · chain C against A, TM-score 0.91
- P14719 · AlphaFold monomer V2.0 prediction for interleukin-1 receptor-like 1 (P14719) · a predicted model of the same protein · chain B against A, TM-score 0.75
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 Q8BVZ5
- Every structure of UniProt P14719
- Every structure of UniProt Q61730
- Elsewhere: RCSB PDB 5VI4 · PDBe 5VI4 · UniProt Q8BVZ5 · UniProt P14719 · UniProt Q61730
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