MolNFT v1 · #165816 · protein

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

6U7F · Aminopeptidase N: “Hcov-229E rbd class IV in complex with human apn”. X-ray diffraction, 2 ligands (NAG, ZN), 17 pockets (best druggability 0.80). MolNFT v1 #165816 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6U7F
Type: protein
Length: 1,993 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, ZN
Pockets: 17 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Aminopeptidase N (EC 3.4.11.2)	protein	897	46% helix, 20% strand	P15144
C	Spike glycoprotein	protein	96	0% helix, 47% strand	—
D	Spike glycoprotein	protein	103	0% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains A, B, C, D
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

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	734	0.80	0.84	85	empty
2	949	0.79	0.80	65	empty
3	597	0.74	0.81	62	empty
4	679	0.74	0.80	77	ZN
5	352	0.70	0.83	33	empty

Interfaces

3 interfaces between chains.

A–B · 1031 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 530 Å² buried · 9 hydrogen bonds · protein-protein
B–D · 519 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 19 glycan, 9 disulfide (N-glycosylation, disulfide).

Compared structures

6U7F · HCoV-229E RBD Class IV in complex with human APN · the same entry in another collection · chain C against C, 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 6U7F · PDBe 6U7F · UniProt P15144

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