MolNFT v1 · #50011 · protein

Crystal structure analysis of HIV-1 subtype C protease complexed with nelfinavir

2R5Q: “Crystal structure analysis of HIV-1 subtype C protease complexed with nelfinavir”. X-ray diffraction, 1 ligand (1UN), 3 pockets (best druggability 0.75). MolNFT v1 #50011 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2R5Q
Type: protein
Length: 396 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: Q50CM2
Ligands: 1UN
Pockets: 3 · best druggability 0.75

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protease	protein	99	4% helix, 55% strand	Q50CM2

Ligands and binding sites

1UN · 2-[2-hydroxy-3-(3-hydroxy-2-methyl-benzoylamino)-4-phenyl sulfanyl-butyl]-decahydro-isoquinoline-3-carboxylic acid tert-butylamide · ligand · 2 copies · chains A, B, C, D

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	385	0.75	0.85	36	1UN
2	386	0.74	0.85	36	1UN
3	158	0.44	0.75	33	empty

Interfaces

4 interfaces between chains.

A–B · 1877 Å² buried · 43 hydrogen bonds · protein-protein
C–D · 1877 Å² buried · 42 hydrogen bonds · protein-protein
A–D · 227 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 100 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2R5Q · Crystal Structure Analysis of HIV-1 Subtype C Protease Complexed with Nelfinavir · 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 Q50CM2
Elsewhere: RCSB PDB 2R5Q · PDBe 2R5Q · UniProt Q50CM2

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