Research workbench
Crystal structure of switch ab Fab and HIL6R in complex with ATP
Analyse Crystal structure of switch ab Fab and HIL6R in complex with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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