MolNFT v1 · #121689 · protein

Prefusion form of the vesicular stomatitis virus glycoprotein G ectodomain

5I2S: “Prefusion form of the vesicular stomatitis virus glycoprotein G ectodomain”. X-ray diffraction, 2 ligands (NAG, YB), 5 pockets (best druggability 0.70). MolNFT v1 #121689 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5I2S
Type: protein
Length: 413 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoprotein G
UniProt: P0C2X0
Ligands: NAG, YB
Pockets: 5 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycoprotein G	protein	413	15% helix, 36% strand	P0C2X0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
YB · Ytterbium (III) ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	57	0.70	0.97	16	empty
2	140	0.60	0.84	25	empty
3	101	0.39	0.77	26	empty
4	77	0.35	0.76	15	empty
5	73	0.31	0.73	14	empty

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5I2S · Prefusion form of the vesicular stomatitis virus glycoprotein G ectodomain · 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 P0C2X0
Elsewhere: RCSB PDB 5I2S · PDBe 5I2S · UniProt P0C2X0

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