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Structural basis of glycan specificity and identification of a novel glycan binding cavity in human P[19] rotavirus

Analyse Structural basis of glycan specificity and identification of a novel glycan… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YMS
Type: protein
Length: 1,283 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Outer capsid protein VP4
UniProt: Q9Q2P6
Ligands: NAG, A2G, GAL
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, G	Outer capsid protein VP4	protein	161	8% helix, 56% strand	Q9Q2P6
C, D, E, F, H	Outer capsid protein VP4	protein	160	10% helix, 58% strand	Q9Q2P6

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains F, H, A, B, C, D, E, G
A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 2 copies · chains F, H
GAL · beta-D-galactopyranose · sugar · 2 copies · chains F, H

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	993	0.79	0.81	148	empty
2	1152	0.75	0.78	115	empty
3	269	0.68	0.84	43	empty
4	404	0.64	0.79	47	empty
5	53	0.27	0.73	17	empty

Interfaces

12 interfaces between chains.

B–G · 659 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 659 Å² buried · 15 hydrogen bonds · protein-protein
E–H · 658 Å² buried · 14 hydrogen bonds · protein-protein
D–F · 641 Å² buried · 14 hydrogen bonds · protein-protein
F–G · 463 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5YMS · Structural basis of glycan specificity and identification of a novel glycan binding… · 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 Q9Q2P6
Elsewhere: RCSB PDB 5YMS · PDBe 5YMS · UniProt Q9Q2P6

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