MolNFT v1 · #76119 · protein

Interleukin-2 mutant D10

3QB1: “Interleukin-2 mutant D10”. X-ray diffraction, 9 pockets (best druggability 0.72). MolNFT v1 #76119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QB1
Type: protein
Length: 947 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-2
UniProt: P60568
Pockets: 9 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 68% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Interleukin-2	protein	124	68% helix, 8% strand	P60568
C	Interleukin-2	protein	119	68% helix, 8% strand	P60568
D	Interleukin-2	protein	110	68% helix, 9% strand	P60568
E	Interleukin-2	protein	117	66% helix, 9% strand	P60568
G	Interleukin-2	protein	111	68% helix, 9% strand	P60568
H	Interleukin-2	protein	118	69% helix, 8% strand	P60568

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1181	0.72	0.76	95	empty
2	367	0.64	0.79	43	empty
3	420	0.62	0.77	34	empty
4	260	0.57	0.78	23	empty
5	278	0.54	0.76	23	empty

Interfaces

9 interfaces between chains.

A–B · 857 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 560 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 497 Å² buried · 4 hydrogen bonds · protein-protein
C–E · 480 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 212 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3QB1 · Interleukin-2 mutant D10 · the same entry in another collection · chain H against H, TM-score 1.00
P60568 · AlphaFold monomer V2.0 prediction for interleukin-2 (P60568) · a predicted model of the same protein · chain D 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 P60568
Elsewhere: RCSB PDB 3QB1 · PDBe 3QB1 · UniProt P60568

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