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Crystal structure of glycoprotein B from herpes simplex virus type I

Analyse Crystal structure of glycoprotein B from herpes simplex virus type I in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5V2S
Type: protein
Length: 705 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein B
UniProt: A1Z0P7
Ligands: NAG
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Envelope glycoprotein B	protein	705	29% helix, 29% strand	A1Z0P7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A

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

Pockets

6 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	184	0.58	0.81	29	empty
2	126	0.45	0.78	20	empty
3	94	0.36	0.74	13	empty
4	72	0.33	0.75	21	empty
5	66	0.32	0.76	16	empty

Modifications

Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

5V2S · Crystal structure of glycoprotein B from Herpes Simplex Virus type I · 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 A1Z0P7
Elsewhere: RCSB PDB 5V2S · PDBe 5V2S · UniProt A1Z0P7

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