Structure of PDB 8p4e Chain B

Receptor sequence

>8p4eB (length=1116) Species: 9823 (Sus scrofa)

EITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPI
DLQPPRYLLKFEQIYLSKPTHWDGAPSPMMPNEARLRNLTYSAPLYVDIT
KTVQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYF
IINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTI
WVSMLARQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPE
MMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKE
MLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLA
GPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKY
SLATGNWGDARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLH
NTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMEN
LEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVS
MIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYS
WQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSM
ILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLY
YPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVD
RGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDG
LIAPGVRVSGDDVIIGKTVTLPENEDRRYTKRDCSTFLRTSETGIVDQVM
VTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTC
EGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNV
QKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDK
IHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLF
EASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLL
FQELMSMSIAPRMMSV

3D structure

• PDB: 8p4e Structural insights into human co-transcriptional capping.
• Chain: B
• Resolution: 3.9 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	rna	B	A464 G465 Q468 Q731 R834 G839 M840 R841 H842 R890 D891 K934 K942 H1053 P1066 R1080	A412 G413 Q416 Q679 R782 G787 M788 R789 H790 R832 D833 K876 K884 H995 P1008 R1022
BS02	dna	B	M200 R222 R385 D386 I489 K494 P498	M165 R187 R339 D340 I437 K442 P446
BS03	dna	B	K436 G1077 R1078 R1085 M1089	K390 G1019 R1020 R1027 M1031
BS04	ZN	B	C1137 C1140	C1079 C1082

Gene Ontology

Molecular Function

• GO:0001055 RNA polymerase II activity
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0032549 ribonucleoside binding
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0001172 RNA-templated transcription
• GO:0006351 DNA-templated transcription
• GO:0006366 transcription by RNA polymerase II

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0000781 chromosome, telomeric region
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005665 RNA polymerase II, core complex

External links

• PDB: RCSB:8p4e, PDBe:8p4e, PDBj:8p4e
• PDBsum: 8p4e
• PubMed: 37369200
• UniProt: I3LGP4