MolNFT v1 · #14275 · protein

Crystal structure of human il-2 complexed with (R)-N-[2-[1- (aminoiminomethyl)-3-piperidinyl]-1-oxoethyl]-4-(phenylethynyl)-L- phenylalanine methyl ester

1M48 · Interleukin-2: “Crystal structure of human il-2 complexed with (R)-N-[2-[1…”. X-ray diffraction, 1 ligand (FRG), 2 pockets (best druggability 0.62). MolNFT v1 #14275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1M48
Type: protein
Length: 249 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Interleukin-2
UniProt: P60568
Ligands: FRG
Pockets: 2 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Interleukin-2	protein	123	66% helix, 3% strand	P60568
B	Interleukin-2	protein	126	64% helix, 3% strand	P60568

Ligands and binding sites

FRG · 2-[3-methyl-4-(N-methyl-guanidino)-butyrylamino]-3-(4-phenylethynyl-phenyl)-propionic acid methyl ester · ligand · 2 copies · chains A, B

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

Pockets

2 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	332	0.62	0.78	28	empty
2	289	0.60	0.79	26	empty

Interfaces

1 interface between chains.

A–B · 705 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

1M48 · Crystal Structure of Human IL-2 Complexed with… · the same entry in another collection · chain A against A, 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 0.95

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 1M48 · PDBe 1M48 · UniProt P60568

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