MolNFT v1 · #39642 · protein

Crystal structure of ad-81 complexed with wild type HIV-1 protease

2I0D: “Crystal structure of ad-81 complexed with wild type HIV-1 protease”. X-ray diffraction, 2 ligands (MUT, PO4), 1 pocket (best druggability 0.70). MolNFT v1 #39642 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2I0D
Type: protein
Length: 198 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protease
UniProt: O38732
Ligands: MUT, PO4
Pockets: 1 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protease	protein	99	4% helix, 55% strand	O38732

Ligands and binding sites

MUT · (5S)-3-(3-acetylphenyl)-N-[(1S,2R)-1-benzyl-2-hydroxy-3-{isobutyl[(4-methoxyphenyl)sulfonyl]amino}propyl]-2-oxo-1,3-oxazolidine-5-carboxamide · ligand · chains A, B
PO4 · Phosphate ion · ion · 4 copies · chains A, B
ACT · Acetate ion · additive · chains 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	369	0.70	0.82	36	MUT

Interfaces

1 interface between chains.

A–B · 1834 Å² buried · 39 hydrogen bonds · protein-protein

Compared structures

2I0D · Crystal structure of AD-81 complexed with wild type HIV-1 protease · 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 O38732
Elsewhere: RCSB PDB 2I0D · PDBe 2I0D · UniProt O38732

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