MolNFT v1 · #1161 · protein

Herpes simplex virus type II protease

1AT3: “Herpes simplex virus type II protease”. X-ray diffraction, 1 ligand (DFP), 4 pockets (best druggability 0.82). MolNFT v1 #1161 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1AT3
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Herpes simplex virus type II protease
UniProt: Q69527
Ligands: DFP
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Herpes simplex virus type II protease	protein	217	33% helix, 22% strand	Q69527

Ligands and binding sites

DFP · Diisopropyl phosphonate · ligand · 2 copies · chains A, B

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

Pockets

4 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	195	0.82	0.96	24	empty
2	74	0.34	0.75	18	empty
3	64	0.34	0.76	15	empty
4	59	0.29	0.75	18	DFP

Interfaces

1 interface between chains.

A–B · 1277 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

1AT3 · Herpes simplex virus type II protease · the same entry in another collection · chain B against B, 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 Q69527
Elsewhere: RCSB PDB 1AT3 · PDBe 1AT3 · UniProt Q69527

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