MolNFT v1 · #165815 · protein

Hcov-229E rbd class III in complex with human apn

6U7E · Aminopeptidase N: “Hcov-229E rbd class III in complex with human apn”. X-ray diffraction, 3 ligands (NAG, BMA, ZN), 20 pockets (best druggability 0.79). MolNFT v1 #165815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6U7E
Type: protein
Length: 2,026 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Aminopeptidase N; Spike glycoprotein
EC: 3.4.11.2
UniProt: P15144
Ligands: NAG, BMA, ZN
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aminopeptidase N (EC 3.4.11.2)	protein	900	46% helix, 19% strand	P15144
C	Spike glycoprotein	protein	109	0% helix, 39% strand	—
D	Spike glycoprotein	protein	117	0% helix, 44% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, C, B, D
BMA · beta-D-mannopyranose · sugar · 2 copies
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	982	0.79	0.80	69	empty
2	431	0.74	0.84	61	empty
3	552	0.73	0.81	64	empty
4	336	0.71	0.84	45	empty
5	325	0.71	0.84	39	empty

Interfaces

3 interfaces between chains.

A–B · 990 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 550 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 525 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 glycan, 10 disulfide (N-glycosylation, disulfide).

Compared structures

6U7E · HCoV-229E RBD Class III in complex with human APN · the same entry in another collection · chain A against A, TM-score 1.00
P15144 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P15144) · a predicted model of the same protein · chain A 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 P15144
Elsewhere: RCSB PDB 6U7E · PDBe 6U7E · UniProt P15144

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.