MolNFT v1 · #176120 · protein
Crystal structure of switch ab Fab and HIL6R in complex with ATP
7DC8 · Switch ab Fab light chain: “Crystal structure of switch ab Fab and HIL6R in complex with ATP”. X-ray diffraction, 2 ligands (ATP, SO4), 10 pockets (best druggability 0.72). MolNFT v1 #176120 on GenesisL1: 3D structure, binding sites…
- PDB
- 7DC8
- Type
- protein
- Length
- 1,212 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Switch ab Fab light chain; Switch ab Fab heavy chain; Interleukin-6 receptor subunit alpha
- UniProt
- P08887
- Ligands
- ATP, SO4
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Switch ab Fab light chain | protein | 212 | 8% helix, 50% strand | — |
| B | Switch ab Fab heavy chain | protein | 209 | 4% helix, 49% strand | — |
| C | Interleukin-6 receptor subunit alpha | protein | 186 | 2% helix, 47% strand | P08887 |
| E | Switch ab Fab heavy chain | protein | 209 | 6% helix, 52% strand | — |
| F | Interleukin-6 receptor subunit alpha | protein | 184 | 2% helix, 47% strand | P08887 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, C, E, F
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, F, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.72 | 0.76 | 102 | ATP, SO4 |
| 2 | 656 | 0.69 | 0.77 | 65 | ATP, SO4 |
| 3 | 717 | 0.65 | 0.74 | 72 | empty |
| 4 | 553 | 0.61 | 0.74 | 53 | empty |
| 5 | 51 | 0.38 | 0.81 | 14 | empty |
Interfaces
7 interfaces between chains.
- C–F · 4215 Ų buried · 75 hydrogen bonds · protein-protein
- D–E · 1674 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1673 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 364 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7DC8 · Crystal structure of Switch Ab Fab and hIL6R in complex with ATP · the same entry in another collection · chain F against F, 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 F against A, TM-score 0.82
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 P08887
- Elsewhere: RCSB PDB 7DC8 · PDBe 7DC8 · UniProt P08887
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