MolNFT v1 · #186325 · protein

Designed stabil-2 SEQ15

7RAA · Interleukin-2: “Designed stabil-2 SEQ15”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.72). MolNFT v1 #186325 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RAA
Type: protein
Length: 496 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-2
UniProt: P60568
Ligands: MG
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 4 distinct chains · 65% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-2	protein	120	64% helix, 8% strand	P60568
B	Interleukin-2	protein	125	67% helix, 3% strand	P60568
C	Interleukin-2	protein	129	59% helix, 3% strand	P60568
D	Interleukin-2	protein	122	68% helix, 3% strand	P60568

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

4 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	1031	0.72	0.76	69	empty
2	161	0.59	0.82	28	empty
3	175	0.44	0.74	26	empty
4	90	0.34	0.74	13	empty

Interfaces

5 interfaces between chains.

A–B · 604 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 504 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 417 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 310 Å² buried · 1 hydrogen bond · protein-protein
B–C · 13 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7RAA · Designed StabIL-2 seq15 · the same entry in another collection · chain D against D, TM-score 1.00
P60568 · AlphaFold monomer V2.0 prediction for interleukin-2 (P60568) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 7RAA · PDBe 7RAA · UniProt P60568

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