Structure of PDB 3ekp Chain B

Receptor sequence

>3ekpB (length=99) Species: 11685 (HIV-1 M:B_ARV2/SF2)

PQITLWKRPIVTIRIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIVGI
GGFVKVRQYDQIPIEICGHKAIGTVLVGPTPANIIGRNLLTQIGCTLNF

3D structure

• PDB: 3ekp Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease.
• Chain: B
• Resolution: 2.15 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	478	B	D25 G27 A28 D30 V48 I50 P81	D25 G27 A28 D30 V48 I50 P81	MOAD: Kd=1.3nM PDBbind-CN: -logKd/Ki=8.89,Kd=1.3nM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3ekp, PDBe:3ekp, PDBj:3ekp
• PDBsum: 3ekp
• PubMed: 22712830
• UniProt: P03369|POL_HV1A2 Gag-Pol polyprotein (Gene Name=gag-pol)