Structure of PDB 3kdb Chain B

Receptor sequence

>3kdbB (length=99) Species: 11686 (Human immunodeficiency virus type 1 (BRU ISOLATE))

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGI
GGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

3D structure

• PDB: 3kdb How much binding affinity can be gained by filling a cavity?
• Chain: B
• Resolution: 1.66 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	006	B	D25 G27 A28 D29 D30 I47 G49 I50 I84	D25 G27 A28 D29 D30 I47 G49 I50 I84	MOAD: Kd=0.14nM PDBbind-CN: -logKd/Ki=9.85,Kd=0.14nM

Gene Ontology

Molecular Function

• GO:0004190 aspartic-type endopeptidase activity

Biological Process

• GO:0006508 proteolysis

External links

• PDB: RCSB:3kdb, PDBe:3kdb, PDBj:3kdb
• PDBsum: 3kdb
• PubMed: 20028396
• UniProt: P03367|POL_HV1BR Gag-Pol polyprotein (Gene Name=gag-pol)