MolNFT v1 · #17967 · protein
Crystal structure of the hexameric human il-6/IL-6 alpha RECEPTOR/GP130 complex
1P9M · Interleukin-6 receptor beta chain: “Crystal structure of the hexameric human il-6/IL-6 alpha RECEPTOR/GP130 complex”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #17967 on GenesisL1: 3D structure, binding sites…
- PDB
- 1P9M
- Type
- protein
- Length
- 662 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-6 receptor beta chain; Interleukin-6; Interleukin-6 receptor alpha chain
- UniProt
- P40189, P05231, P08887
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-6 receptor beta chain | protein | 298 | 2% helix, 34% strand | P40189 |
| B | Interleukin-6 | protein | 163 | 62% helix, 0% strand | P05231 |
| C | Interleukin-6 receptor alpha chain | protein | 201 | 0% helix, 41% strand | P08887 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 962 | 0.79 | 0.81 | 93 | empty |
| 2 | 114 | 0.55 | 0.84 | 29 | empty |
| 3 | 51 | 0.48 | 0.86 | 12 | empty |
| 4 | 98 | 0.40 | 0.76 | 17 | empty |
| 5 | 64 | 0.39 | 0.79 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–C · 819 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 784 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 689 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1P9M · Crystal structure of the hexameric human IL-6/IL-6 alpha receptor/gp130 complex · the same entry in another collection · chain A against A, TM-score 1.00
- P08887 · AlphaFold monomer V2.0 prediction for interleukin-6 receptor subunit alpha (P08887) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P05231 · AlphaFold monomer V2.0 prediction for interleukin-6 (P05231) · a predicted model of the same protein · chain B against A, TM-score 0.93
- P40189 · AlphaFold monomer V2.0 prediction for interleukin-6 receptor subunit beta (P40189) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P40189
- Every structure of UniProt P05231
- Every structure of UniProt P08887
- Elsewhere: RCSB PDB 1P9M · PDBe 1P9M · UniProt P40189 · UniProt P05231 · UniProt P08887
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