Structure of PDB 9ja1 Chain B

Receptor sequence

>9ja1B (length=1100) Species: 4932 (Saccharomyces cerevisiae)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKVFIGR
LPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSA
GNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTI
KATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVE
DGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFL
GYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDI
FRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRY
TYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM
SCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRN
PARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVED
DESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESI
LIAMQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPD
HNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAME
YLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYM
DQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDV
IIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKI
PQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTV
AHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMY
NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRS
RDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIA
KLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRD

3D structure

• PDB: 9ja1 The RNA polymerase II elongation complex from Saccharomyces cerevisiae
• Chain: B
• Resolution: 2.98 Å

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	rna	B	A477 Q481 Q776 K979 K987	A391 Q395 Q666 K856 K864
BS02	dna	B	A462 R857 R942 R1122 R1129 M1133	A376 R747 R819 R999 R1006 M1010
BS03	ZN	B	C1163 C1182	C1040 C1059
BS04	ATP	B	R766 K987 R1020	R656 K864 R897

External links

• PDB: RCSB:9ja1, PDBe:9ja1, PDBj:9ja1
• PDBsum: 9ja1
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)