MolNFT v1 · #151940 · protein

Structure of EV71 complexed with its receptor SCARB2

6I2K · Polyprotein: “Structure of EV71 complexed with its receptor SCARB2”. Electron microscopy, 4 ligands (906, NAG, MAN), 20 pockets (best druggability 0.86). MolNFT v1 #151940 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6I2K
Type: protein
Length: 1,227 residues
Chains: 5
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyprotein; Lysosome membrane protein 2
UniProt: D4QGA2, D4QGA3, Q6YLE3, Q14108
Ligands: 906, NAG, MAN, BMA
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 5 distinct chains · 12% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polyprotein	protein	290	5% helix, 28% strand	—
B	Polyprotein	protein	245	10% helix, 38% strand	D4QGA2
C	Polyprotein	protein	242	13% helix, 33% strand	D4QGA3
D	Polyprotein	protein	58	10% helix, 9% strand	Q6YLE3
E	Lysosome membrane protein 2	protein	392	17% helix, 29% strand	Q14108

Ligands and binding sites

906 · 1-(2-aminopyridin-4-yl)-3-[(3S)-5-{4-[(E)-(ethoxyimino)methyl]phenoxy}-3-methylpentyl]imidazolidin-2-one · ligand · chains A, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains E
MAN · alpha-D-mannopyranose · sugar · 11 copies · chains E, B
BMA · beta-D-mannopyranose · sugar · 4 copies · chains E

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

Pockets

20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1052	0.86	0.86	99	empty
2	414	0.80	0.88	56	906
3	83	0.55	0.86	24	empty
4	147	0.53	0.80	23	NAG
5	174	0.52	0.79	34	empty

Interfaces

8 interfaces between chains.

A–C · 4073 Å² buried · 62 hydrogen bonds · protein-protein
A–B · 2451 Å² buried · 34 hydrogen bonds · protein-protein
B–C · 1769 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 1558 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1080 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

6I2K · Structure of EV71 complexed with its receptor SCARB2 · the same entry in another collection · chain A against A, TM-score 1.00
Q14108 · AlphaFold monomer V2.0 prediction for lysosome membrane protein 2 (Q14108) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 D4QGA2
Every structure of UniProt D4QGA3
Every structure of UniProt Q6YLE3
Every structure of UniProt Q14108
Elsewhere: RCSB PDB 6I2K · PDBe 6I2K · UniProt D4QGA2 · UniProt D4QGA3 · UniProt Q6YLE3 · UniProt Q14108

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