Structure of PDB 8v5r Chain A

Receptor sequence

>8v5rA (length=944) Species: 9606 (Homo sapiens)

GQLRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQP
AVPLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKP
PAWAWAEGWTRYGPEGEAVPVAIPEERALVFAVAVCLAEGTCPTLAVAIS
PSAWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTDWQEQLVVGHNVSFD
RAHIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKQGISSWDW
LDISSVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCA
QDVWATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAE
AQGTYEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQ
KEDLGPCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKL
CPRLDDPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPG
RHHGNGPYNDVDIPGCWFFKLPHKDGNSCNVGSPFAKDFLPKMEDGTLQA
GSGPRALEINKMISFWRNAHKRISSQMVVWLPRSALPRAVIRHPDYDEEG
LYGAILPQVVTAGTITRRAVEPTWLTASNARPDRVGSELKAMVQAPPGYT
LVGADVDSQELWIAAVLGDAHFAGMHGCTAFGWMTLQGRKSRGTDLHSKT
ATTVGISREHAKIFNYGRIYGAGQPFAERLLMQFNHRLTQQEAAEKAQQM
YAATKGLWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEE
FMTSRVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLV
REEDRYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRK
EVTMDCKTPSNPTGMERRYGIPQGEALDIYQIIELTKGSLEKRS

3D structure

• PDB: 8v5r Coordinated DNA polymerization by Pol gamma and the region of LonP1 regulated proteolysis.
• Chain: A
• Resolution: 3.0 Å

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	A	R562 R579 H754 N761 G763 A767 K768 L860 T861 A862 S863 R869 H1134	R436 R453 H523 N530 G532 A536 K537 L625 T626 A627 S628 R634 H843
BS02	dna	A	S306 R309 K561 M596 R597 N803 K806 R807 T849 G952 Y955 G956 A957 F961 T1094	S232 R235 K435 M470 R471 N568 K571 R572 T614 G717 Y720 G721 A722 F726 T803
BS03	MG	A	D890 V891 D1135	D655 V656 D844
BS04	D3T	A	D892 H932 R943 K947 Y951 D1135	D657 H697 R708 K712 Y716 D844

Gene Ontology

Molecular Function

• GO:0002020 protease binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0016787 hydrolase activity
• GO:0016829 lyase activity
• GO:0051575 5'-deoxyribose-5-phosphate lyase activity

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006264 mitochondrial DNA replication
• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006287 base-excision repair, gap-filling
• GO:0045004 DNA replication proofreading
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0000262 mitochondrial chromosome
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005760 gamma DNA polymerase complex
• GO:0032991 protein-containing complex
• GO:0042645 mitochondrial nucleoid
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8v5r, PDBe:8v5r, PDBj:8v5r
• PDBsum: 8v5r
• PubMed: 38932681
• UniProt: P54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)