MolNFT v1 · #111560 · protein

Mouse il-2 bound to S4B6 Fab fragment

4YUE · S4B6 Fab heavy chain: “Mouse il-2 bound to S4B6 Fab fragment”. X-ray diffraction, 6 pockets (best druggability 0.66). MolNFT v1 #111560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4YUE
Type: protein
Length: 541 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S4B6 Fab heavy chain; S4B6 Fab light chain; Interleukin-2
UniProt: P04351
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	S4B6 Fab heavy chain	protein	223	11% helix, 51% strand	—
L	S4B6 Fab light chain	protein	214	6% helix, 50% strand	—
C	Interleukin-2	protein	104	58% helix, 10% strand	P04351

Ligands and binding sites

GOL · Glycerol · additive · chains H, L

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	356	0.66	0.80	43	empty
2	651	0.64	0.74	70	GOL
3	149	0.44	0.76	27	empty
4	90	0.41	0.78	21	empty
5	73	0.33	0.75	18	empty

Interfaces

3 interfaces between chains.

H–L · 1915 Å² buried · 14 hydrogen bonds · protein-protein
H–C · 456 Å² buried · 7 hydrogen bonds · protein-protein
L–C · 421 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4YUE · Mouse IL-2 Bound to S4B6 Fab Fragment · the same entry in another collection · chain H against H, TM-score 1.00
P04351 · AlphaFold monomer V2.0 prediction for interleukin-2 (P04351) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P04351
Elsewhere: RCSB PDB 4YUE · PDBe 4YUE · UniProt P04351

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.