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Crystal structure of guanarito virus GP2 in the post-fusion conformation

Analyse Crystal structure of guanarito virus GP2 in the post-fusion conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C53
Type: protein
Length: 318 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pre-glycoprotein polyprotein gp complex
UniProt: A1A3Z2
Ligands: NAG, MAN, BMA
Pockets: 5 · best druggability 0.39

Structure

x-ray diffraction · 3 distinct chains · 63% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pre-glycoprotein polyprotein gp complex	protein	101	63% helix, 2% strand	A1A3Z2
B	Pre-glycoprotein polyprotein gp complex	protein	115	63% helix, 2% strand	A1A3Z2
C	Pre-glycoprotein polyprotein gp complex	protein	102	62% helix, 2% strand	A1A3Z2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C
MAN · alpha-D-mannopyranose · sugar · 12 copies
BMA · beta-D-mannopyranose · sugar · 4 copies

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	151	0.39	0.73	23	empty
2	100	0.37	0.74	16	empty
3	64	0.33	0.75	14	empty
4	73	0.30	0.73	17	empty
5	50	0.26	0.74	18	empty

Interfaces

3 interfaces between chains.

A–B · 2094 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 1784 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1745 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan (N-glycosylation).

Compared structures

4C53 · Crystal Structure of Guanarito virus GP2 in the post-fusion conformation · 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 A1A3Z2
Elsewhere: RCSB PDB 4C53 · PDBe 4C53 · UniProt A1A3Z2

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