Research workbench
Structure reveals function of the dual variable domain immunoglobulin (dvd-ig) molecule
Analyse Structure reveals function of the dual variable domain immunoglobulin (dvd-ig)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HJJ
- Type
- protein
- Length
- 825 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Interleukin-18; Anti-IL12 anti-IL18 dfab heavy chain; Anti-IL12 anti-IL18 dfab light chain
- UniProt
- Q14116
- Ligands
- SO4, CL
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Interleukin-18 | protein | 157 | 8% helix, 48% strand | Q14116 |
| H | Anti-IL12 anti-IL18 dfab heavy chain | protein | 341 | 5% helix, 51% strand | — |
| L | Anti-IL12 anti-IL18 dfab light chain | protein | 327 | 5% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains H
- CL · Chloride ion · ion · chains L
- GOL · Glycerol · additive · 2 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.75 | 0.80 | 109 | empty |
| 2 | 255 | 0.57 | 0.78 | 35 | empty |
| 3 | 319 | 0.56 | 0.76 | 33 | empty |
| 4 | 231 | 0.52 | 0.76 | 30 | empty |
| 5 | 164 | 0.44 | 0.75 | 31 | empty |
Interfaces
3 interfaces between chains.
- H–L · 3245 Ų buried · 27 hydrogen bonds · protein-protein
- A–H · 998 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 209 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4HJJ · Structure Reveals Function of the Dual Variable Domain Immunoglobulin (DVD-Ig) Molecule · the same entry in another collection · chain A against A, TM-score 1.00
- Q14116 · AlphaFold monomer V2.0 prediction for interleukin-18 (Q14116) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q14116
- Elsewhere: RCSB PDB 4HJJ · PDBe 4HJJ · UniProt Q14116
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