Structure of PDB 2xyf Chain B

Receptor sequence

>2xyfB (length=99) Species: 11683 (Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE))

PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIPIEICGHKAIGTVLVGPTPTNVIGRNLLTQIGCTLNF

3D structure

• PDB: 2xyf HIV-1 Protease Inhibitors with a Tertiary Alcohol Containing Transition-State Mimic and Various P2 and P1' Substituents
• Chain: B
• Resolution: 1.8 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	G40	B	L123 D125 G127 A128 D129 G148 G149 F153 P181 T182	L23 D25 G27 A28 D29 G48 G49 F53 P81 T82	PDBbind-CN: -logKd/Ki=8.44,Ki=3.6nM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:2xyf, PDBe:2xyf, PDBj:2xyf
• PDBsum: 2xyf
• UniProt: P12499|POL_HV1Z2 Gag-Pol polyprotein (Gene Name=gag-pol)