MolNFT v1 · #54484 · protein

Crystal structure of anti-il-15 antibody in complex with human il-15

2XQB · Interleukin 15: “Crystal structure of anti-il-15 antibody in complex with human il-15”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.56). MolNFT v1 #54484 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 2XQB
Type: protein
Length: 534 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin 15; Anti-il-15 antibody
UniProt: P40933
Ligands: SO4
Pockets: 7 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 19% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin 15	protein	105	66% helix, 6% strand	P40933
H	Anti-il-15 antibody	protein	227	8% helix, 49% strand	—
L	Anti-il-15 antibody	protein	202	6% helix, 51% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains H, A, L

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

Pockets

7 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	191	0.56	0.80	29	empty
2	419	0.56	0.74	63	empty
3	137	0.52	0.80	30	empty
4	82	0.46	0.81	19	empty
5	95	0.45	0.80	20	empty

Interfaces

3 interfaces between chains.

H–L · 1764 Å² buried · 16 hydrogen bonds · protein-protein
A–H · 769 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 383 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

2XQB · Crystal Structure of anti-IL-15 Antibody in Complex with human IL-15 · the same entry in another collection · chain A against A, TM-score 1.00
P40933 · AlphaFold monomer V2.0 prediction for interleukin-15 (P40933) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P40933
Elsewhere: RCSB PDB 2XQB · PDBe 2XQB · UniProt P40933

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