Structure of PDB 4hdp Chain B

Receptor sequence

>4hdpB (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGV
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

3D structure

• PDB: 4hdp Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease.
• Chain: B
• Resolution: 1.22 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	G52	B	D25 G27 A28 D29 D30 G48 G49 V50	D25 G27 A28 D29 D30 G48 G49 V50	MOAD: Ki=30.9nM PDBbind-CN: -logKd/Ki=7.51,Ki=30.9nM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:4hdp, PDBe:4hdp, PDBj:4hdp
• PDBsum: 4hdp
• PubMed: 23298236
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)