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Crystal structure of the il-15/IL-15RA complex

Analyse Crystal structure of the il-15/IL-15RA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z3R
Type: protein
Length: 1,534 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-15; Interleukin-15 receptor alpha chain
UniProt: P40933, Q13261
Pockets: 20 · best druggability 0.77

Structure

x-ray diffraction · 11 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-15	protein	113	66% helix, 5% strand	P40933
B	Interleukin-15 receptor alpha chain	protein	74	9% helix, 35% strand	Q13261
C, I, K, M	Interleukin-15	protein	116	69% helix, 5% strand	P40933
D, N	Interleukin-15 receptor alpha chain	protein	76	0% helix, 34% strand	Q13261
E, G	Interleukin-15	protein	119	68% helix, 7% strand	P40933
F	Interleukin-15 receptor alpha chain	protein	73	10% helix, 38% strand	Q13261
H	Interleukin-15 receptor alpha chain	protein	77	5% helix, 31% strand	Q13261
J	Interleukin-15 receptor alpha chain	protein	78	5% helix, 31% strand	Q13261
L	Interleukin-15 receptor alpha chain	protein	75	7% helix, 35% strand	Q13261
O	Interleukin-15	protein	118	64% helix, 5% strand	P40933
P	Interleukin-15 receptor alpha chain	protein	72	6% helix, 39% strand	Q13261

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains N, O, A, D

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

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.77	0.83	65	empty
2	671	0.77	0.83	57	empty
3	567	0.77	0.84	53	empty
4	678	0.77	0.82	75	empty
5	395	0.57	0.74	40	empty

Interfaces

28 interfaces between chains.

G–K · 752 Å² buried · 8 hydrogen bonds · protein-protein
C–O · 709 Å² buried · 9 hydrogen bonds · protein-protein
G–H · 666 Å² buried · 15 hydrogen bonds · protein-protein
C–D · 663 Å² buried · 15 hydrogen bonds · protein-protein
I–J · 660 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 32 disulfide (disulfide).

Compared structures

2Z3R · Crystal structure of the IL-15/IL-15Ra complex · the same entry in another collection · chain K against K, TM-score 1.00

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
Every structure of UniProt Q13261
Elsewhere: RCSB PDB 2Z3R · PDBe 2Z3R · UniProt P40933 · UniProt Q13261

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