Structure of PDB 6dcf Chain D Binding Site BS03

Receptor Information
>6dcf Chain D (length=1176) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIF
GPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVT
HIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLE
AEMAVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGE
REMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYF
TGAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAF
QQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNN
RLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSL
SDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELF
KPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAP
TLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQ
AEARILMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAA
TKDAPEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFE
NGWKPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAER
FPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVQKQEILERHEAEADA
IERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVKS
GATADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGRDAHVETSA
FARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGITTVKVRSVLTCTS
ATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTGGLPRVQELFEA
RVPRNKAPIADVAGRVRLEESDKFFKITIVPDDGGEEVVYDKLSKRQRLR
VIGTEGVLSDGDHVEVGDQLMEGAADPHEVLRVQGPREVQIHLVKEVQEV
YRAQGVSIHDKHIEVIVRQMLRRVTIIDSEFLPGSLTERAEFEAENAGRP
VLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIG
KLIPAGTGISRYRNIQVQPTEEARAA
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 chain6dcf 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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PDB6dcf Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
Resolution3.45 Å
Binding residue
(original residue number in PDB)		D535 D537 D539
Binding residue
(residue number reindexed from 1)		D533 D535 D537
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:6dcf, PDBe:6dcf, PDBj:6dcf
PDBsum6dcf
PubMed30297823
UniProtA0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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