Crystal structure of HIV-1 LM/HS clade A/E CRF01 GP120 core in complex with bnm-III-170

Structure

x-ray diffraction · 1 distinct chain · 17% helix, 38% strand (DSSP).

Ligands and binding sites

• 5VG · ~{N}'-[(1~{R},2~{R})-2-(carbamimidamidomethyl)-5-(methylaminomethyl)-2,3-dihydro-1~{H}-inden-1-yl]-~{N}-(4-chloranyl-3-fluoranyl-phenyl)ethanediamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
• EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Modifications

Observed in the structure: 10 glycan, 8 disulfide (N-glycosylation, disulfide).

Compared structures

• 6UT1 · Crystal structure of HIV-1 LM/HS clade A/E CRF01 GP120 core in complex with bnm-III-170 · 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 A0A0M3KKW9
• Elsewhere: RCSB PDB 6UT1 · PDBe 6UT1 · UniProt A0A0M3KKW9