Structure of PDB 5iyd Chain A

Receptor sequence
>5iydA (length=1454) Species: 9606 (Homo sapiens) [Search protein sequence]
DSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMD
PRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRC
VCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGGH
GGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDE
ECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLA
DIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQK
SGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVP
RSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRF
HPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWST
FRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSN
RPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILK
PRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVE
NGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLL
IEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGN
TLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINI
SQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGL
TPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRN
SINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALR
RTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPC
NLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSR
QAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIA
HPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINIS
KKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNP
QSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQI
AEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDD
DVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKAL
QEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERE
LYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCS
FEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCK
YGME
3D structure
PDB5iyd Near-atomic resolution visualization of human transcription promoter opening.
ChainA
Resolution3.9 Å
3D
structure
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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 A R190 S1131 K1132 H1417 R1421 R159 S1100 K1101 H1386 R1390
BS02 dna A P323 K331 K344 K346 R358 R364 Q461 T854 A855 E1433 P292 K300 K313 K315 R327 R333 Q430 T823 A824 E1402
BS03 MG A D497 G498 D499 D466 G467 D468
BS04 MG A D495 F496 D497 D464 F465 D466
BS05 ZN A R70 C71 R61 C62
BS06 ZN A C111 C114 C102 C105
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0001055 RNA polymerase II activity
GO:0003677 DNA 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:0008270 zinc ion binding
GO:0016787 hydrolase activity
GO:0019900 kinase binding
GO:0031625 ubiquitin protein ligase binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
GO:0050436 microfibril binding
GO:1990841 promoter-specific chromatin binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006353 DNA-templated transcription termination
GO:0006355 regulation of DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0033120 positive regulation of RNA splicing
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0005694 chromosome
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0031981 nuclear lumen
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5iyd, PDBe:5iyd, PDBj:5iyd
PDBsum5iyd
PubMed27193682
UniProtP24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)

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