MolNFT v1 · #125368 · protein

IL13 in complex with tralokinumab

5L6Y · Interleukin-13: “IL13 in complex with tralokinumab”. X-ray diffraction, 6 pockets (best druggability 0.62). MolNFT v1 #125368 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L6Y
Type: protein
Length: 538 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-13; Tralokinumab Fab digest vh; Tralokiumab Fab digest vl
UniProt: P35225
Pockets: 6 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 15% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Interleukin-13	protein	94	55% helix, 6% strand	P35225
H	Tralokinumab Fab digest vh	protein	232	6% helix, 47% strand	—
L	Tralokiumab Fab digest vl	protein	212	8% helix, 49% strand	—

Ligands and binding sites

FMT · Formic acid · additive · 15 copies · chains H, L, C

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	299	0.62	0.80	49	empty
2	90	0.55	0.85	18	FMT
3	410	0.55	0.73	54	FMT
4	74	0.38	0.78	18	empty
5	97	0.38	0.76	21	FMT

Interfaces

3 interfaces between chains.

H–L · 1852 Å² buried · 11 hydrogen bonds · protein-protein
C–L · 536 Å² buried · 8 hydrogen bonds · protein-protein
C–H · 221 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5L6Y · il13 in complex with tralokinumab · the same entry in another collection · chain C against C, TM-score 1.00
P35225 · AlphaFold monomer V2.0 prediction for interleukin-13 (P35225) · a predicted model of the same protein · chain C against A, TM-score 0.94

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 5L6Y · PDBe 5L6Y · UniProt P35225

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