MolNFT v1 · #123916 · protein

Cryoem structure of the native empty particle of a human rhinovirus C

5JZG · Capsid protein VP1: “Cryoem structure of the native empty particle of a human rhinovirus C”. Electron microscopy, 8 pockets (best druggability 0.59). MolNFT v1 #123916 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JZG
Type: protein
Length: 764 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP3; Capsid protein VP0
UniProt: E5D8F2
Pockets: 8 · best druggability 0.59

Structure

electron microscopy · 3 distinct chains · 7% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	226	8% helix, 29% strand	E5D8F2
B	Capsid protein VP3	protein	235	9% helix, 30% strand	E5D8F2
C	Capsid protein VP0	protein	303	6% helix, 29% strand	E5D8F2

Pockets

8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	379	0.59	0.76	39	empty
2	335	0.57	0.76	37	empty
3	64	0.51	0.85	19	empty
4	182	0.43	0.74	32	empty
5	146	0.43	0.75	30	empty

Interfaces

3 interfaces between chains.

A–B · 3083 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 3025 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 2178 Å² buried · 22 hydrogen bonds · protein-protein

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 E5D8F2
Elsewhere: RCSB PDB 5JZG · PDBe 5JZG · UniProt E5D8F2

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