Structure of PDB 7lbm Chain A Binding Site BS01

Receptor Information

>7lbm Chain A (length=1455) Species: 9606 (Homo sapiens)

DSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMD
PRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRC
VCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGGC
GRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECF
VLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIV
KINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGR
PLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSI
AANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPK
PSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRL
NLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPV
MGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRP
LWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGE
LIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEG
HTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLR
QTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQV
IAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPT
EFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSIN
QVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTL
QEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLL
RMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQ
ENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPG
EMVGALAAQSLGEPATKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSA
RDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYE
MPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFN
DDNAEKLVLRIRIMNSDENKMEVVDKMDDDVFLRCIESNMLTDMTLQGIE
QISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDV
DPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLC
DTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMK
GVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMESPTSPSYSPTSPSYYSP
TSPSY

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 7lbm Chain A Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lbm Structure of the human Mediator-bound transcription preinitiation complex.
• Resolution: 4.8 Å
• Binding residue (original residue number in PDB): R460 D495
• Binding residue (residue number reindexed from 1): R426 D461
• Annotation score: 1

Enzymatic activity

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

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

External links

• PDB: RCSB:7lbm, PDBe:7lbm, PDBj:7lbm
• PDBsum: 7lbm
• PubMed: 33707221
• UniProt: P24928|RPB1_HUMAN DNA-directed RNA polymerase II subunit RPB1 (Gene Name=POLR2A)