MolNFT v1 · #140801 · protein

Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens

5YMU · Outer capsid protein VP4: “Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens”. X-ray diffraction, 2 pockets (best druggability 0.78). MolNFT v1 #140801 on GenesisL1: 3D…

PDB: 5YMU
Type: protein
Length: 640 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein VP4
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Outer capsid protein VP4	protein	160	10% helix, 57% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	982	0.78	0.80	93	empty
2	102	0.36	0.74	18	empty

Interfaces

4 interfaces between chains.

A–C · 550 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 320 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 99 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 93 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5YMU · Functional and structural characterization of P[19] rotavirus VP8* interaction with… · 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
Elsewhere: RCSB PDB 5YMU · PDBe 5YMU

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