MolNFT v1 · #50513 · protein

HIV-1 pr resistant mutant + lpv

2RKF · Protease retropepsin: “HIV-1 pr resistant mutant + lpv”. X-ray diffraction, 2 ligands (AB1, SO4), 1 pocket (best druggability 0.69). MolNFT v1 #50513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2RKF
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease retropepsin
EC: 3.4.23.16
UniProt: A0F7J4
Ligands: AB1, SO4
Pockets: 1 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease retropepsin (EC 3.4.23.16)	protein	99	7% helix, 54% strand	A0F7J4

Ligands and binding sites

AB1 · N-{1-benzyl-4-[2-(2,6-dimethyl-phenoxy)-acetylamino]-3-hydroxy-5-phenyl-pentyl}-3-methyl-2-(2-oxo-tetrahydro-pyrimidin-1-yl)-butyramide · ligand · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 2 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	411	0.69	0.81	41	AB1

Interfaces

1 interface between chains.

A–B · 1783 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

2RKF · HIV-1 PR resistant mutant + LPV · 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 A0F7J4
Elsewhere: RCSB PDB 2RKF · PDBe 2RKF · UniProt A0F7J4

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