Structure of PDB 8s5n Chain A

Receptor sequence

>8s5nA (length=1423) Species: 9823 (Sus scrofa)

SACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDP
RQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCV
CFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGCGR
YQPRIRRSGLELYAEWKKILLSPERVHEIFKRISDEECFVLGMEPRYARP
EWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQ
NGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKG
KEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVT
PFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYK
VERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNAD
FDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAV
RKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLI
IPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSL
GTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIAD
SKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRIL
NDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEG
KRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGRE
GLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDG
LAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSN
AHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFH
INPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHL
RSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSL
GEPATQMTLNKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERA
KDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDV
ARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEK
LVLRIRIMNSDENKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQT
DNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVE
IFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAI
TRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLA
PAGTGCFDLLLDAEKCKYGMEIP

3D structure

• PDB: 8s5n Three-step mechanism of promoter escape by RNA polymerase II
• Chain: A
• Resolution: 3.4 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

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	Y145 R190 K1132 H1417	Y135 R154 K1078 H1353
BS02	rna	A	V264 V265 M266 R334 R460 P462 N493 D495 D497 D499	V219 V220 M221 R289 R415 P417 N448 D450 D452 D454
BS03	dna	A	R193 M266 P323 S332 K344 K346 R358 R364 Q461 P462 T854 A855 Y859 R862 R1416 E1434	R157 M221 P278 S287 K299 K301 R313 R319 Q416 P417 T809 A810 Y814 R817 R1352 E1370
BS04	ZN	A	C71 C81 H84	C61 C71 H74
BS05	ZN	A	C111 C114 C154	C101 C104 C144
BS06	MG	A	D495 D497 D499	D450 D452 D454

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0031981 nuclear lumen
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:8s5n, PDBe:8s5n, PDBj:8s5n
• PDBsum: 8s5n
• PubMed: 38604172
• UniProt: A0A7M4DUC2