Structure of PDB 5iyd Chain B

Receptor sequence

>5iydB (length=1165) Species: 9606 (Homo sapiens)

YDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIV
EDAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMM
PNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRST
YCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFA
KKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVAT
LPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAF
VIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCET
KKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFK
NLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKA
HQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMV
CPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPA
AIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIRE
REIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVAS
GVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCAS
IIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLV
TTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSV
FYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVR
VSGDDVIIGKTVTLPENEDELESTNRRYTKRDCSTFLRTSETGIVDQVMV
TLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCE
GITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQ
KISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKI
HSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFE
ASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLF
QELMSMSIAPRMMSV

3D structure

• PDB: 5iyd Near-atomic resolution visualization of human transcription promoter opening.
• Chain: B
• Resolution: 3.9 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.48: RNA-directed RNA polymerase.
  2.7.7.6: DNA-directed RNA polymerase.
  3.1.13.-

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	B	F208 K211 E220 P231 T232 W236 Y262 R385 Q461 A462 I489 G493 K494 L495 K497 P498	F199 K202 E211 P222 T223 W227 Y253 R376 Q452 A453 I480 G484 K485 L486 K488 P489
BS02	dna	B	N188 S190 Y446 Q456 T746 K815 K1058 R1078 R1085	N179 S181 Y437 Q447 T737 K806 K1049 R1069 R1076
BS03	rna	B	Q468 E516 K934 K942	Q459 E507 K925 K933
BS04	ZN	B	C1137 R1138	C1128 R1129

Gene Ontology

Molecular Function

• GO:0001055 RNA polymerase II activity
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003723 RNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0003968 RNA-dependent RNA polymerase activity
• GO:0005515 protein binding
• GO:0016787 hydrolase 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
• GO:0016020 membrane

External links

• PDB: RCSB:5iyd, PDBe:5iyd, PDBj:5iyd
• PDBsum: 5iyd
• PubMed: 27193682
• UniProt: P30876|RPB2_HUMAN DNA-directed RNA polymerase II subunit RPB2 (Gene Name=POLR2B)