Structure of PDB 6ika Chain C

Receptor sequence

>6ikaC (length=553) Species: 11676 (Human immunodeficiency virus 1)

PISPIETVPVKLKPGMDGPKVKQWPLTEEKIKALVEICTEMEKEGKISKI
GPENPYNTPVFAIKKKDSTKWRKLVDFRELNKRTQDFWEVQLGIPHPAGL
KQKKSVTVLDVSAAFYSVPLDKDFRKYTAFTIPSINNETPGIRYQYNVLP
MGWKGSPALLQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSDLEIGQHRT
KIEELRQHLLRWGFTTPDKKHQKEPPFLWMGYELHPDKWTVQPIVLPEKD
SWTVNDIQKLVGKLNWASQIYAGIKVRQLSKLLRGTKALTEVVPLTEEAE
LELAENREILKEPVHGVYYDPSKDLIAEIQKQGQGQWTYQIYQEPFKNLK
TGKYARMKGAHTNDVKQLTEAVQKIATESIVIWGKTPKFKLPIQKETWEA
WWTEYWQATWIPEWEFVNTPPLVKLWYQLEKEPIIGAETFYVDGAANRET
KLGKAGYVTDRGRQKVVPLTDTTNQKTELQAIHLALQDSGLEVNIVTDSQ
YALGIIQAQPDKSESELVSQIIEQLIKKEKVYLAWVPAHKGIGGNEQVDK
LVS

3D structure

• PDB: 6ika Active-site deformation in the structure of HIV-1 RT with HBV-associated septuple amino acid substitutions rationalizes the differential susceptibility of HIV-1 and HBV against 4'-modified nucleoside RT inhibitors.
• Chain: C
• Resolution: 2.598 Å

Enzymatic activity

• Enzyme Commision number: 3.1.26.13: retroviral ribonuclease H.

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	dna	C	W24 F61 L74 R78 N81 E89 Q91 I94 G152 P157 Y183 M184 D185 M230 G231 N255 Q258 K259 G262 K263 W266 S280 R284 K353 G359 H361 K374 R448 T473 Q475 Y501	W24 F61 L74 R78 N81 E89 Q91 I94 G152 P157 Y183 M184 D185 M230 G231 N255 Q258 K259 G262 K263 W266 S280 R284 K353 G359 H361 K374 R448 T473 Q475 Y501
BS02	ET9	C	R72 S112 A113 F115 M184 D185	R72 S112 A113 F115 M184 D185
BS03	MG	C	D110 V111 D185	D110 V111 D185

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003964 RNA-directed DNA polymerase activity
• GO:0004523 RNA-DNA hybrid ribonuclease activity

Biological Process

• GO:0006278 RNA-templated DNA biosynthetic process

External links

• PDB: RCSB:6ika, PDBe:6ika, PDBj:6ika
• PDBsum: 6ika
• PubMed: 30648556
• UniProt: D3XFN7