MolNFT v1 · #69955 · protein
Crystal structure of the complex between il-13 and H2L6 Fab
3L5X · H2L6 light chain: “Crystal structure of the complex between il-13 and H2L6 Fab”. X-ray diffraction, 4 pockets (best druggability 0.61). MolNFT v1 #69955 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3L5X
- Type
- protein
- Length
- 539 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H2L6 light chain; H2L6 heavy chain; Interleukin-13
- UniProt
- P35225
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | H2L6 light chain | protein | 214 | 5% helix, 50% strand | — |
| H | H2L6 heavy chain | protein | 224 | 8% helix, 50% strand | — |
| A | Interleukin-13 | protein | 101 | 52% helix, 6% strand | P35225 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains L
- GOL · Glycerol · additive · chains L, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.61 | 0.75 | 60 | empty |
| 2 | 206 | 0.49 | 0.75 | 29 | empty |
| 3 | 71 | 0.32 | 0.75 | 19 | empty |
| 4 | 57 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1974 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 477 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 151 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).
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 P35225
- Elsewhere: RCSB PDB 3L5X · PDBe 3L5X · UniProt P35225
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