Structure of PDB 3nf8 Chain B

Receptor sequence
>3nf8B (length=149) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence]
SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAG
RWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEDGIPYNPQSQGVIESMNK
ELKKIIGQVRDQAEHLKTAVQMAVFIHNHKRKGYSAGERIVDIIATDIQ
3D structure
PDB3nf8 Structural basis for a new mechanism of inhibition of HIV-1 integrase identified by fragment screening and structure-based design
ChainB
Resolution1.9 Å
3D
structure
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Enzymatic activity
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 CDQ B H185 S195 G197 E198 H129 S135 G137 E138 PDBbind-CN: -logKd/Ki=3.00,IC50>1000uM
BS02 CDQ B Q95 Y99 T125 A129 W132 Q39 Y43 T69 A73 W76 PDBbind-CN: -logKd/Ki=3.00,IC50>1000uM
BS03 CDQ B R107 P109 I204 D207 R51 P53 I144 D147 PDBbind-CN: -logKd/Ki=3.00,IC50>1000uM
BS04 CDQ B E170 H171 K173 T174 M178 E114 H115 K117 T118 M122 PDBbind-CN: -logKd/Ki=3.00,IC50>1000uM
BS05 CDQ B V79 G82 I84 V150 M154 E157 L158 H183 V23 G26 I28 V94 M98 E101 L102 H127 PDBbind-CN: -logKd/Ki=3.00,IC50>1000uM
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
Biological Process
GO:0015074 DNA integration

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3nf8, PDBe:3nf8, PDBj:3nf8
PDBsum3nf8
PubMed21602613
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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