Structure of PDB 6vdk Chain C

Receptor sequence
>6vdkC (length=270) Species: 11676 (Human immunodeficiency virus 1) [Search protein sequence]
FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIATDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVV
IQDNSDIKVVPRRKAKIIRD
3D structure
PDB6vdk A Peptide Derived from Lens Epithelium-Derived Growth Factor Stimulates HIV-1 DNA Integration and Facilitates Intasome Structural Studies.
ChainC
Resolution4.5 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 dna C H51 G52 Q53 V54 G140 I141 Q146 S147 G149 V150 M154 E157 H51 G52 Q53 V54 G140 I141 Q146 S147 G149 V150 M154 E157
BS02 dna C L45 K46 G47 L45 K46 G47
BS03 dna C A49 H51 A49 H51
BS04 MG C D64 D116 D64 D116
BS05 MG C D64 E152 D64 E152
BS06 DLU C D116 P145 Q146 E152 D116 P145 Q146 E152
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0008270 zinc ion binding
Biological Process
GO:0015074 DNA integration

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Molecular Function
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Biological Process
External links
PDB RCSB:6vdk, PDBe:6vdk, PDBj:6vdk
PDBsum6vdk
PubMed32061936
UniProtP12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)

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