MolNFT v1 · #146396 · protein

Structure of a de novo designed interleukin-2/INTERLEUKIN-15 mimetic

6DG6 · Neoleukin-2/15: “Structure of a de novo designed interleukin-2/INTERLEUKIN-15 mimetic”. X-ray diffraction, 4 pockets (best druggability 0.57). MolNFT v1 #146396 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DG6
Type: protein
Length: 597 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neoleukin-2/15
Pockets: 4 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 85% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E	Neoleukin-2/15	protein	100	86% helix, 0% strand	—
C	Neoleukin-2/15	protein	100	81% helix, 0% strand	—
D	Neoleukin-2/15	protein	100	83% helix, 0% strand	—
F	Neoleukin-2/15	protein	97	89% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	348	0.57	0.75	27	empty
2	200	0.50	0.76	18	empty
3	144	0.48	0.78	21	empty
4	83	0.42	0.79	18	empty

Interfaces

6 interfaces between chains.

A–E · 610 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 455 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 291 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 214 Å² buried · 1 hydrogen bond · protein-protein
E–F · 205 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6DG6 · Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 6DG6 · PDBe 6DG6

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