Structure of PDB 8p0k Chain A

Receptor sequence

>8p0kA (length=1277) Species: 10245 (Vaccinia virus)

AVISKVTYSLYDQKEINATDIIISHVKNDDDIGTVKDGRLGAMDGALCKT
CGKTELECFGHWGKVSIYKTHIVKPEFISEIIRLLNHICIHCGLLRSREP
YSDDINLKELSGHALRRLKDKILSKKKSCWNSECMQPYQKITFSKKKVCF
VNKLDDINVPNSLIYQKLISIHEKFWPLLEIHQYPANLFYTDYFPIPPLI
IRPAISETNELTYLLGMIVKNCNLNADEQVIQKAVIEYDDIKIISNNTTS
INLSYITSGKNNMIRSYIVARRKDQTARSVIGPSTSITVNEVGMPAYIRN
TLTEKIFVNAFTVDKVKQLLASNQVKFYFNKRLNQLTRIRQGKFIKNKIH
LLPGDWVEVAVQEYTSIIFGRQPSLHRYNVIASSIRATEGDTIKISPGIA
NSQNADFDGDEEWMILEQNPKAVIEQSILMYPTTLLKHDIHGAPVYGSIQ
DEIVAAYSLFRIQDLCLDEVLNILGKYGREFDPKGKCKFSGKDIYTYLIG
EKINYPGLLKDGEIIANDVDSNFVVAMRHLSLAGLLSDHKSNVEGINFII
KSSYVFKRYLSIYGFGVTFKDLRPNSTFTNKLEAINVEKIELIKEAYAKY
LNDVRDGKIVPLSKALEADYVESMLSNLTNLNIREIEEHMRQTLIDDPDN
NLLKMAKAGYKVNPTELMYILGTYGQQRIDGEPAETRVLGRVLPYYLPDS
KDPEGRGYILNSLTKGLTGSQYYFSMLVARSQSTDIVCETSRTGTLARKI
IKKMEDMVVDGYGQVVIGNTLIKYAANYTKILGSVCKPVDLIYPDESMTW
YLEISALWNKIKQGFVYSQKQKLAKKTLAPFNFLVFVKPTTEDNAIKVKD
LYDMIHNVIDDVREKYFFTVSNIDFMEYIFLTHLNPSRIRITKETAITIF
EKFYEKLNYTLGGGTPIGIISAQVLSEKFTQQALSSFHTTEKSGAVKQKL
GFNEFNNLTNLSKNKTEIITLVSDDISKLQSVKINFEFVCLGELNPNITL
RKETDKYVVDIIVNRLYIKRAEITELVVEYMIERFISFSVIVKEWGMETF
IEDEDNIRFTVYLNFVEPEELNLSKFMMVLPGAANKGKISKFKIPISDYT
GYDDFNQTKKLNKMTVELMNLKELGSFDLENVNVYPGVWNTYDIFGIEAA
REYLCEAMLNTYGEGFDYLYQPCDLLASLLCASYEPESVNKFKFGAASTL
KRATFGDNKALLNAALHKKSEPINDNSSCHFFSKVPNIGTGYYKYFIDLG
LLMRMERKLSDKISSQKIKEMEETEDF

3D structure

• PDB: 8p0k Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex (CASP target)
• Chain: A
• Resolution: 2.64 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	A	K141 K154	K140 K153
BS02	dna	A	K269 T749 S750 G753 T754	K260 T740 S741 G744 T745
BS03	MG	A	D415 D417 D419	D406 D408 D410
BS04	ZN	A	C49 C59 H62	C48 C58 H61
BS05	ZN	A	C90 C93 C130 C135	C89 C92 C129 C134

Gene Ontology

Molecular Function

• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0044423 virion component

External links

• PDB: RCSB:8p0k, PDBe:8p0k, PDBj:8p0k
• PDBsum: 8p0k
• UniProt: P20504|RP147_VACCC DNA-directed RNA polymerase 147 kDa polypeptide (Gene Name=OPG105)