MolNFT v1 · #181900 · protein

HIV-1 protease wt (NL4-3) in complex with LR3-68

7M9J: “HIV-1 protease wt (NL4-3) in complex with LR3-68”. X-ray diffraction, 2 ligands (YWM, SO4), 1 pocket (best druggability 0.71). MolNFT v1 #181900 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7M9J
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
EC: 3.4.23.16
UniProt: P03367
Ligands: YWM, SO4
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Protease (EC 3.4.23.16)	protein	99	4% helix, 55% strand	P03367

Ligands and binding sites

YWM · Diethyl [(4-{(2S,3R)-2-[({[(3r,3as,6ar)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxy-4-[{4-[(1S)-1-hydroxyethyl]benzene-1-sulfonyl}(2-methylpropyl)amino]butyl}phenoxy) methyl]phosphonate · ligand · chains B, A
SO4 · Sulfate ion · ion · 3 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	426	0.71	0.82	38	YWM

Interfaces

1 interface between chains.

B–A · 1837 Å² buried · 41 hydrogen bonds · protein-protein

Compared structures

7M9J · HIV-1 Protease WT (NL4-3) in Complex with LR3-68 · 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 P03367
Elsewhere: RCSB PDB 7M9J · PDBe 7M9J · UniProt P03367

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