MolNFT v1 · #119378 · protein
Biophysical and cellular characterisation of a junctional epitope antibody that locks il-6 and GP80 together in a stable complex: implications for new therapeutic strategies
5FUC · Interleukin-6: “Biophysical and cellular characterisation of a junctional epitope antibody that locks il-6 and GP80 together…”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.74). MolNFT v1 #119378 on GenesisL1…
- PDB
- 5FUC
- Type
- protein
- Length
- 943 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-6; Interleukin-6 receptor subunit alpha, interleukin-6 receptor; VHH6
- UniProt
- P05231, D6R9R8, P08887
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-6 | protein | 152 | 72% helix, 0% strand | P05231 |
| B | Interleukin-6 | protein | 160 | 68% helix, 0% strand | P05231 |
| C | Interleukin-6 receptor subunit alpha, interleukin-6 receptor | protein | 199 | 2% helix, 43% strand | D6R9R8, P08887 |
| D | Interleukin-6 receptor subunit alpha, interleukin-6 receptor | protein | 198 | 0% helix, 44% strand | D6R9R8, P08887 |
| E | VHH6 | protein | 110 | 11% helix, 30% strand | — |
| V | VHH6 | protein | 124 | 15% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, E, D, V
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 552 | 0.74 | 0.82 | 72 | empty |
| 2 | 559 | 0.71 | 0.80 | 61 | empty |
| 3 | 105 | 0.41 | 0.77 | 18 | empty |
| 4 | 103 | 0.40 | 0.76 | 21 | empty |
| 5 | 59 | 0.34 | 0.78 | 15 | empty |
Interfaces
8 interfaces between chains.
- B–C · 991 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 646 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 539 Ų buried · 10 hydrogen bonds · protein-protein
- D–V · 524 Ų buried · 16 hydrogen bonds · protein-protein
- A–V · 514 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5FUC · Biophysical and cellular characterisation of a junctional epitope antibody that locks… · the same entry in another collection · chain V against V, TM-score 1.00
- P05231 · AlphaFold monomer V2.0 prediction for interleukin-6 (P05231) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P08887 · AlphaFold monomer V2.0 prediction for interleukin-6 receptor subunit alpha (P08887) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 P05231
- Every structure of UniProt D6R9R8
- Every structure of UniProt P08887
- Elsewhere: RCSB PDB 5FUC · PDBe 5FUC · UniProt P05231 · UniProt D6R9R8 · UniProt P08887
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