Structure of PDB 6c04 Chain D Binding Site BS04

Receptor Information
>6c04 Chain D (length=1267) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GAMLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFC
EKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELA
APVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNEL
STLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVR
DGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRY
GEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKV
VAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVI
NRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRP
LKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMA
LELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLL
NRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLS
AEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGE
YQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEA
ELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIIN
DLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDH
YEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNP
IITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLE
YFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIV
VELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPE
IDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIV
AAQSIGEPGTQLTMITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGE
RFYKITIVPDDGGEEVVYDKISKRQRLRVFKRVLSDGDHVEVGQQLMEGS
ADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRV
TIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASL
ATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGIN
RYRNIAVQPTEEARAAA
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 chain6c04 Chain D Residue 2002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6c04 Fidaxomicin jamsMycobacterium tuberculosisRNA polymerase motions needed for initiation via RbpA contacts.
Resolution3.27 Å
Binding residue
(original residue number in PDB)		D535 D537 D539
Binding residue
(residue number reindexed from 1)		D537 D539 D541
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
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6c04, PDBe:6c04, PDBj:6c04
PDBsum6c04
PubMed29480804
UniProtP9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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