Structure of PDB 6kop Chain D

Receptor sequence

>6kopD (length=1263) Species: 83332 (Mycobacterium tuberculosis H37Rv)

LDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKI
FGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPV
THIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTL
EAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGG
EREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEY
FTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAA
FQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRN
NRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKS
LSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALEL
FKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRA
PTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEA
QAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQP
ASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELF
GHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLA
ERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEE
RADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIIT
IVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFI
NTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVEL
AERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDA
LLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQ
SIGEPGTQLTMGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKI
TIVPDDGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEG
SADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRR
VTIIDSGSTEFLPGSLIDRAEFEAENRRVVAEAAGRPVLMGITKASLATD
SWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYR
NIAVQPTEEARAA

3D structure

• PDB: 6kop RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
• Chain: D
• Resolution: 3.303 Å

Enzymatic activity

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

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	D	P111 S112 Y116 P122 K123 R291 K294 R1038	P110 S111 Y115 P121 K122 R290 K293 R1024
BS02	dna	D	V110 Q287 L330 R386 K409 R427 A501 T867 A868 Y872 Q1227 E1228	V109 Q286 L329 R385 K408 R426 A500 T866 A867 Y871 Q1209 E1210
BS03	rna	D	R397 D537 D539	R396 D536 D538
BS04	ZN	D	C60 C62 C75 C78	C59 C61 C74 C77
BS05	ZN	D	C891 C968 C978	C890 C967 C977
BS06	MG	D	D535 D537 D539	D534 D536 D538

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

External links

• PDB: RCSB:6kop, PDBe:6kop, PDBj:6kop
• PDBsum: 6kop
• PubMed: 32127479
• UniProt: P9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)