Research workbench

HIV-1 protease NL4-3 wt in complex with LR2-35

Analyse HIV-1 protease NL4-3 wt in complex with LR2-35 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PJM
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease NL4-3
UniProt: Q8ULI9
Ligands: OQV, SO4
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 56% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease NL4-3	protein	99	7% helix, 56% strand	Q8ULI9

Ligands and binding sites

OQV · (3r,3as,6ar)-hexahydrofuro[2,3-b]furan-3-yl [(2S,3S, 5S)-3-hydroxy-5-{[N-(methoxycarbonyl)-3-methyl-L-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate · ligand · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	365	0.71	0.83	32	OQV

Interfaces

1 interface between chains.

A–B · 1823 Å² buried · 42 hydrogen bonds · protein-protein

Compared structures

6PJM · HIV-1 Protease NL4-3 WT in Complex with LR2-35 · 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 Q8ULI9
Elsewhere: RCSB PDB 6PJM · PDBe 6PJM · UniProt Q8ULI9

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