Structure of PDB 2aod Chain B

Receptor sequence

>2aodB (length=99) Species: 11682 (Human immunodeficiency virus type 1 (BH5 ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

3D structure

• PDB: 2aod Molecular basis for substrate recognition and drug resistance from 1.1 to 1.6 angstroms resolution crystal structures of HIV-1 protease mutants with substrate analogs.
• Chain: B
• Resolution: 1.4 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D125 T126 G127
• 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	2NC	B	D125 G127 A128 D129 D130 I147 G148 P181 V182	D25 G27 A28 D29 D30 I47 G48 P81 V82	PDBbind-CN: -logKd/Ki=5.66,Ki=2.17uM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:2aod, PDBe:2aod, PDBj:2aod
• PDBsum: 2aod
• PubMed: 16218957
• UniProt: P04587|POL_HV1B5 Gag-Pol polyprotein (Gene Name=gag-pol)