Research workbench

Human il-2/FAB complex

Analyse Human il-2/FAB complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UTZ
Type: protein
Length: 2,251 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab 5111 heavy chain; Fab 5111 light chain; Interleukin-2
UniProt: Q6GMX6, Q6IPQ0, P60568
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 10 distinct chains · 23% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab 5111 heavy chain	protein	224	5% helix, 50% strand	Q6GMX6
L, K	Fab 5111 light chain	protein	215	7% helix, 50% strand	Q6IPQ0
D	Interleukin-2	protein	126	67% helix, 4% strand	P60568
B	Fab 5111 heavy chain	protein	220	5% helix, 51% strand	Q6GMX6
C, G	Fab 5111 light chain	protein	213	7% helix, 50% strand	Q6IPQ0
A	Interleukin-2	protein	131	64% helix, 8% strand	P60568
F	Fab 5111 heavy chain	protein	223	5% helix, 51% strand	Q6GMX6
E	Interleukin-2	protein	126	67% helix, 9% strand	P60568
J	Fab 5111 heavy chain	protein	219	5% helix, 53% strand	Q6GMX6
I	Interleukin-2	protein	126	67% helix, 9% strand	P60568

Ligands and binding sites

GOL · Glycerol · additive · 5 copies · chains L, B, C, G, J

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	877	0.81	0.84	120	GOL
2	477	0.76	0.84	69	empty
3	838	0.68	0.75	84	empty
4	567	0.63	0.75	56	empty
5	355	0.60	0.77	43	empty

Interfaces

21 interfaces between chains.

J–K · 1796 Å² buried · 16 hydrogen bonds · protein-protein
H–L · 1721 Å² buried · 15 hydrogen bonds · protein-protein
F–G · 1673 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1670 Å² buried · 17 hydrogen bonds · protein-protein
F–J · 1145 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 4 modified (disulfide, cyclization).

Compared structures

5UTZ · Human IL-2/Fab complex · the same entry in another collection · chain I against I, 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 Q6GMX6
Every structure of UniProt Q6IPQ0
Every structure of UniProt P60568
Elsewhere: RCSB PDB 5UTZ · PDBe 5UTZ · UniProt Q6GMX6 · UniProt Q6IPQ0 · UniProt P60568

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