Research workbench

SIV protease crystallized with peptide product

Analyse SIV protease crystallized with peptide product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1YTH
Type: protein
Length: 202 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV protease; Peptide product
EC: 3.4.23.16
UniProt: P03369
Ligands: ACE
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 55% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV protease (EC 3.4.23.16)	protein	99	4% helix, 56% strand	P03369
I	Peptide product	protein	4	0% helix, 50% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B, I

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	162	0.61	0.84	24	empty

Interfaces

3 interfaces between chains.

A–B · 1845 Å² buried · 45 hydrogen bonds · protein-protein
A–I · 358 Å² buried · 15 hydrogen bonds · protein-protein
B–I · 236 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1YTH · SIV protease crystallized with peptide product · 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 P03369
Elsewhere: RCSB PDB 1YTH · PDBe 1YTH · UniProt P03369

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