Structure of PDB 6yxu Chain D Binding Site BS03

Receptor Information
>6yxu Chain D (length=1269) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPT
RDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIW
YFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEAEM
AVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGEREM
RQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYFTGA
MGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQQS
GNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLK
RLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDL
LKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPF
VMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLH
RLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEA
RILMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAATKD
APEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFENGW
KPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERFPM
IVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPQKQEILERHEAEADAI
ERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVKSG
ATGNLTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTHGA
RKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGP
DGTLIRDAHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAG
ITTVKVRSVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEP
GTQLTMRTFDIVGGLPRVQELFEARVPRNKAPIADVAGRVRLEESDKFFK
ITIVPDDGGEEVVYDKLSKRQRLRVITHEDGTEGVLSDGDHVEVGDQLME
GAADPHEVLRVQGPREVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQMLR
RVTIIDSGSTEFLPGSLTERAEFEAENRRVVAEGGEPAAGRPVLMGITKA
SLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTG
ISRYRNIQVQPTEEARAAA
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6yxu Chain D Residue 2003 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6yxu Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.
Resolution3.08 Å
Binding residue
(original residue number in PDB)		D535 D537 D539
Binding residue
(residue number reindexed from 1)		D530 D532 D534
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6yxu, PDBe:6yxu, PDBj:6yxu
PDBsum6yxu
PubMed33339823
UniProtA0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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