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Crystal structure of the complex between il-13 and H2L6 Fab

Analyse Crystal structure of the complex between il-13 and H2L6 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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.

Pocket	Volume (Å³)	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 Å² buried · 15 hydrogen bonds · protein-protein
H–A · 477 Å² buried · 8 hydrogen bonds · protein-protein
L–A · 151 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 modified (disulfide, cyclization).

Compared structures

3L5X · Crystal structure of the complex between IL-13 and H2L6 FAB · the same entry in another collection · chain L against L, TM-score 1.00
P35225 · AlphaFold monomer V2.0 prediction for interleukin-13 (P35225) · 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 P35225
Elsewhere: RCSB PDB 3L5X · PDBe 3L5X · UniProt P35225

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