MolNFT v1 · #114072 · protein

Crystal structure of a darunavir resistant HIV-1 protease

5B18: “Crystal structure of a darunavir resistant HIV-1 protease”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.72). MolNFT v1 #114072 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5B18
Type: protein
Length: 396 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
Ligands: CL
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protease	protein	99	7% helix, 51% strand	—

Ligands and binding sites

CL · Chloride ion · ion · 4 copies · chains A, C, B, D
ACT · Acetate ion · additive · 2 copies · chains B, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	549	0.72	0.80	55	empty
2	525	0.69	0.79	43	empty

Interfaces

4 interfaces between chains.

C–D · 1602 Å² buried · 35 hydrogen bonds · protein-protein
A–B · 1540 Å² buried · 40 hydrogen bonds · protein-protein
A–C · 369 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 44 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5B18 · Crystal Structure of a Darunavir Resistant HIV-1 Protease · the same entry in another collection · chain D against D, 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
Elsewhere: RCSB PDB 5B18 · PDBe 5B18

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