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Structure of a C-terminally truncated form of glycoprotein D from HSV- 1

Analyse Structure of a C-terminally truncated form of glycoprotein D from HSV- 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L2G
Type: protein
Length: 968 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycoprotein D
UniProt: P57083
Ligands: NAG
Pockets: 8 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D, C	Glycoprotein D	protein	242	15% helix, 33% strand	P57083

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, D, C

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

Pockets

8 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	771	0.69	0.76	47	empty
2	725	0.69	0.76	48	empty
3	106	0.39	0.75	18	empty
4	92	0.37	0.76	17	empty
5	87	0.35	0.75	16	empty

Interfaces

2 interfaces between chains.

A–B · 1302 Å² buried · 18 hydrogen bonds · protein-protein
D–C · 1286 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

1L2G · Structure of a C-terminally truncated form of glycoprotein D from HSV-1 · 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 P57083
Elsewhere: RCSB PDB 1L2G · PDBe 1L2G · UniProt P57083

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