Structure of PDB 3cyw Chain B

Receptor sequence

>3cywB (length=99) Species: 11682 (Human immunodeficiency virus type 1 (BH5 ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIVGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

3D structure

• PDB: 3cyw Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.
• Chain: B
• Resolution: 1.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D25 T26 G27
• Catalytic site (residue number reindexed from 1): D25 T26 G27
• Enzyme Commision number: 2.7.7.-
  2.7.7.49: RNA-directed DNA polymerase.
  2.7.7.7: DNA-directed DNA polymerase.
  3.1.-.-
  3.1.13.2: exoribonuclease H.
  3.1.26.13: retroviral ribonuclease H.
  3.4.23.16: HIV-1 retropepsin.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	017	B	D25 G27 A28 D29 V48 G49 I50	D25 G27 A28 D29 V48 G49 I50	PDBbind-CN: -logKd/Ki=7.77,Ki=17nM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3cyw, PDBe:3cyw, PDBj:3cyw
• PDBsum: 3cyw
• PubMed: 18597780
• UniProt: P04587|POL_HV1B5 Gag-Pol polyprotein (Gene Name=gag-pol)