MolNFT v1 · #124766 · protein

Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable fragment of an astrovirus neutralizing antibody at 3.24-a resolution

5KOV · Capsid polyprotein VP90: “Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single chain variable…”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.72). MolNFT v1 #124766 on…

PDB: 5KOV
Type: protein
Length: 3,263 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid polyprotein VP90; Pl-2 scfv chain
UniProt: Q82446
Ligands: NAG
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 12 distinct chains · 2% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, H, M, T	Capsid polyprotein VP90	protein	216	1% helix, 46% strand	Q82446
C, K	Pl-2 scfv chain	protein	223	1% helix, 50% strand	—
E	Pl-2 scfv chain	protein	224	3% helix, 50% strand	—
B	Capsid polyprotein VP90	protein	218	1% helix, 46% strand	Q82446
I	Pl-2 scfv chain	protein	225	3% helix, 48% strand	—
G	Capsid polyprotein VP90	protein	219	1% helix, 44% strand	Q82446
N	Capsid polyprotein VP90	protein	217	1% helix, 42% strand	Q82446
Q	Pl-2 scfv chain	protein	93	0% helix, 28% strand	—
O	Pl-2 scfv chain	protein	212	1% helix, 47% strand	—
S	Capsid polyprotein VP90	protein	218	1% helix, 45% strand	Q82446
W	Pl-2 scfv chain	protein	105	0% helix, 26% strand	—
U	Pl-2 scfv chain	protein	222	3% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, E, K, I

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	781	0.72	0.78	101	empty
2	574	0.66	0.76	57	empty
3	547	0.63	0.76	46	empty
4	356	0.57	0.75	30	empty
5	113	0.56	0.84	25	empty

Interfaces

28 interfaces between chains.

A–B · 2015 Å² buried · 32 hydrogen bonds · protein-protein
N–M · 1995 Å² buried · 37 hydrogen bonds · protein-protein
S–T · 1988 Å² buried · 37 hydrogen bonds · protein-protein
H–G · 1985 Å² buried · 38 hydrogen bonds · protein-protein
O–M · 917 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

5KOV · Crystal structure of the human astrovirus 2 capsid protein spike in complex with a single… · 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
Every structure of UniProt Q82446
Elsewhere: RCSB PDB 5KOV · PDBe 5KOV · UniProt Q82446

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