Structure of PDB 8yfq Chain B

Receptor sequence

>8yfqB (length=1146) Species: 460519 (Komagataella phaffii)

DDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLIL
INKRYEIRFGKIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDME
KSMFTSIDGNKVHIGKVPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYF
VINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSRLIST
MQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHIC
YDENDWQMLEMLKPCIEEGFVIQDKEVALDFIGRRGSAALGIRREKRIQY
AKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHF
GKKRLDLAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKST
TITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTP
IGLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPII
NFLEEWGMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRR
SGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRIT
KEHIRKIQQGYDDDEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDL
QTRSLNDTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQS
PRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLAKTQAMEYLKF
RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK
RFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGK
TTPIPHTKRDASTPLRSTENGIVDQVLLTTNQEGLKFVKVRMRTTKVPQI
GDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHL
IECLLSKVGSIRGYEGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGH
TGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDG
GLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLK
KNQFECRSCKNKTNIYQLHIPYAAKLLFQELMAMNIAPRLYTERSG

3D structure

• PDB: 8yfq Structural basis of eukaryotic transcription termination by the Rat1 exonuclease complex.
• Chain: B
• Resolution: 3.3 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	dna	B	R427 R942 R1122 R1129 M1133	R383 R866 R1046 R1053 M1057
BS02	rna	B	Q474 Q776 R884 H887 H932 H1097 R1124	Q430 Q712 R820 H823 H856 H1021 R1048
BS03	ZN	B	C1163 C1166 C1182 C1185	C1087 C1090 C1106 C1109

External links

• PDB: RCSB:8yfq, PDBe:8yfq, PDBj:8yfq
• PDBsum: 8yfq
• PubMed: 39245712
• UniProt: C4QZQ7