MolNFT v1 · #104974 · protein
Extracellular domains of mouse il-3 beta receptor
4QQV · Interleukin-3 receptor class 2 subunit beta: “Extracellular domains of mouse il-3 beta receptor”. X-ray diffraction, 1 ligand (NAG), 15 pockets (best druggability 0.73). MolNFT v1 #104974 on GenesisL1: 3D structure, binding sites…
- PDB
- 4QQV
- Type
- protein
- Length
- 1,512 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-3 receptor class 2 subunit beta
- UniProt
- P26954
- Ligands
- NAG
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-3 receptor class 2 subunit beta | protein | 399 | 4% helix, 40% strand | P26954 |
| B | Interleukin-3 receptor class 2 subunit beta | protein | 395 | 4% helix, 36% strand | P26954 |
| C | Interleukin-3 receptor class 2 subunit beta | protein | 402 | 4% helix, 37% strand | P26954 |
| D | Interleukin-3 receptor class 2 subunit beta | protein | 316 | 3% helix, 44% strand | P26954 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.73 | 0.82 | 52 | empty |
| 2 | 516 | 0.73 | 0.81 | 63 | empty |
| 3 | 892 | 0.68 | 0.75 | 96 | empty |
| 4 | 121 | 0.65 | 0.88 | 24 | empty |
| 5 | 174 | 0.63 | 0.84 | 35 | empty |
Interfaces
6 interfaces between chains.
- A–B · 5414 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 5225 Ų buried · 71 hydrogen bonds · protein-protein
- B–C · 1098 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4QQV · Extracellular domains of mouse IL-3 beta receptor · the same entry in another collection · chain D against D, TM-score 1.00
- P26954 · AlphaFold monomer V2.0 prediction for interleukin-3 receptor class 2 subunit beta (P26954) · a predicted model of the same protein · chain D against A, TM-score 0.94
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 P26954
- Elsewhere: RCSB PDB 4QQV · PDBe 4QQV · UniProt P26954
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