Research workbench
Structure of interleukin-6 in complex with a camelid Fab fragment
Analyse Structure of interleukin-6 in complex with a camelid Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O9H
- Type
- protein
- Length
- 563 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-6; Heavy chain of the camelid Fab fragment 61H7; Light chain of the camelid…
- UniProt
- P05231
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-6 | protein | 152 | 70% helix, 0% strand | P05231 |
| H | Heavy chain of the camelid Fab fragment 61H7 | protein | 200 | 5% helix, 50% strand | — |
| L | Light chain of the camelid Fab fragment 61H7 | protein | 211 | 9% helix, 51% strand | — |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.70 | 0.98 | 20 | empty |
| 2 | 287 | 0.50 | 0.73 | 45 | empty |
| 3 | 69 | 0.47 | 0.83 | 15 | empty |
| 4 | 104 | 0.42 | 0.77 | 17 | empty |
| 5 | 101 | 0.36 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1640 Ų buried · 12 hydrogen bonds · protein-protein
- A–H · 584 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 412 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
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
- Elsewhere: RCSB PDB 4O9H · PDBe 4O9H · UniProt P05231
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