Structure of PDB 6s1m Chain A

Receptor sequence

>6s1mA (length=1010) Species: 9606 (Homo sapiens)

RWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVSVPVLRAFGVTDEGFS
VCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRDSRGGRELTGPA
VLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRVAGL
GTPSFAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEKATQCQL
EADVLWSDVVSHPPEGPWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQ
ICSLGLRWGEPEPFLRLALTLRPCAPILGAKVQSYEKEEDLLQAWSTFIR
IMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPFLGRVAGLCSNIRDSSF
QSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFHFLGEHS
IITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTGVP
LSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKG
YYDVPIATLDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPT
GDEFVKTSVRKGLLPQILENLLSARKRAKAELAKETDPLRRQVLDGRQLA
LKVSANSVYGFTGAQVGKLPCLEISQSVTGFGRQMIEKTKQLVESKYTVE
NGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAADWVSGHFPSPIRL
EFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLVAN
LVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAAS
DYAGKQAHVELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDP
LFVLEHSLPIDTQYYLEQQLAKPLLRIFEPILGEGRAEAVLLRGDHTRCK
TVLGLLAFAKRRNCCIGCRTVLSHQGAVCEFCQPRESELYQKEVSHLNAL
EERFSRLWTQCQRCQGSLHEDVICTSRDCPIFYMRKKVRKDLEDQEQLLR
RFGPPGPEAW

3D structure

• PDB: 6s1m Structure of the processive human Pol delta holoenzyme.
• Chain: A
• Resolution: 4.27 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-

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	T756 D757 G828 R833 R834 E886 T888 S892	T664 D665 G736 R741 R742 E794 T796 S800
BS02	dna	A	R224 Q551 Q552 D580 G583 G702 V708 K806 A935 Y936 R968	R138 Q459 Q460 D488 G491 G610 V616 K714 A843 Y844 R876
BS03	SF4	A	C1058 C1061 C1071 C1076 I1078 F1079	C961 C964 C974 C979 I981 F982
BS04	TTP	A	S605 L606 Y607 R667 K694 N698	S513 L514 Y515 R575 K602 N606

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003684 damaged DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0004527 exonuclease activity
• GO:0005515 protein binding
• GO:0008296 3'-5'-DNA exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0019899 enzyme binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0000731 DNA synthesis involved in DNA repair
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006281 DNA repair
• GO:0006287 base-excision repair, gap-filling
• GO:0006297 nucleotide-excision repair, DNA gap filling
• GO:0009411 response to UV
• GO:0034644 cellular response to UV
• GO:0045004 DNA replication proofreading
• GO:0055089 fatty acid homeostasis
• GO:0070987 error-free translesion synthesis
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0000109 nucleotide-excision repair complex
• GO:0000781 chromosome, telomeric region
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005829 cytosol
• GO:0016020 membrane
• GO:0016235 aggresome
• GO:0043625 delta DNA polymerase complex

External links

• PDB: RCSB:6s1m, PDBe:6s1m, PDBj:6s1m
• PDBsum: 6s1m
• PubMed: 32111820
• UniProt: P28340|DPOD1_HUMAN DNA polymerase delta catalytic subunit (Gene Name=POLD1)