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Structure of the large protease resistant upper domain of VP5, the major capsid protein of herpes simplex virus-1

Analyse Structure of the large protease resistant upper domain of VP5, the major capsid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NO7
Type: protein
Length: 1,076 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein
UniProt: P06491
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein	protein	542	40% helix, 8% strand	P06491
B	Major capsid protein	protein	534	40% helix, 8% strand	P06491

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	798	0.82	0.85	82	empty
2	537	0.77	0.84	67	empty
3	153	0.62	0.85	20	empty
4	154	0.62	0.85	31	empty
5	155	0.56	0.81	20	empty

Interfaces

1 interface between chains.

A–B · 1061 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

1NO7 · Structure of the Large Protease Resistant Upper Domain of VP5, the Major Capsid Protein… · 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 P06491
Elsewhere: RCSB PDB 1NO7 · PDBe 1NO7 · UniProt P06491

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