Structure of PDB 5u1c Chain C

Receptor sequence

>5u1cC (length=251) Species: 2287 (Saccharolobus solfataricus)

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAM
HGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYF
LLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGV
IQSMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERI
VDIIFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKII
R

3D structure

• PDB: 5u1c Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.
• Chain: C
• Resolution: 3.9 Å

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 G140 I141 N144 Q146 S147 S153 K156 E157 W243 E246 G247 A248 R263	H51 G52 Q53 G140 I141 N144 Q146 S147 S153 K156 E157 W225 E228 G229 A230 R245
BS02	dna	C	Q146 Q152 K156 K159 R231	Q146 Q152 K156 K159 R213
BS03	dna	C	D116 N117 G118 P142 Y143	D116 N117 G118 P142 Y143
BS04	dna	C	K46 K266	K46 K248
BS05	dna	C	A49 M50 H51 T93 S119 S123 R228	A49 M50 H51 T93 S119 S123 R210
BS06	ZN	C	H12 H16	H12 H16
BS07	MG	C	D64 D116	D64 D116

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0004521 RNA endonuclease activity
• GO:0008270 zinc ion binding

Biological Process

• GO:0015074 DNA integration

External links

• PDB: RCSB:5u1c, PDBe:5u1c, PDBj:5u1c
• PDBsum: 5u1c
• PubMed: 28059769
• UniProt: P12497|POL_HV1N5 Gag-Pol polyprotein (Gene Name=gag-pol)