MolNFT v1 · #73913 · protein

Crystal structure of 6S-98S fiv protease with darunavir bound

3OGP: “Crystal structure of 6S-98S fiv protease with darunavir bound”. X-ray diffraction, 1 ligand (017), 3 pockets (best druggability 0.77). MolNFT v1 #73913 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3OGP
Type: protein
Length: 224 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fiv protease
EC: 3.4.23.-
UniProt: P16088
Ligands: 017
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Fiv protease (EC 3.4.23.-)	protein	112	6% helix, 53% strand	P16088

Ligands and binding sites

017 · (3r,3as,6ar)-hexahydrofuro[2,3-b]furan-3-yl(1s,2r)-3-[[(4-aminophenyl)sulfonyl](isobutyl)amino]-1-benzyl-2-hydroxypropylcarbamate · ligand · 2 copies · chains A, B
DMS · Dimethyl sulfoxide · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	400	0.77	0.86	41	017
2	80	0.40	0.78	17	empty
3	56	0.33	0.77	13	empty

Interfaces

1 interface between chains.

A–B · 1820 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

3OGP · Crystal Structure of 6s-98S FIV Protease with Darunavir bound · 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 P16088
Elsewhere: RCSB PDB 3OGP · PDBe 3OGP · UniProt P16088

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