Structure of PDB 8f5w Chain A

Receptor sequence

>8f5wA (length=1010) Species: 9823 (Sus scrofa)

PVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHC
EKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFIT
SISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINI
GGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISC
ASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLG
VKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQG
FYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSAL
RCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGR
IVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALS
PIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWY
IHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAA
PTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGP
GQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWME
LSRKAEASGADALELNLSSPHGLACGQDPELVRNICRWVRQAVQIPFFAK
LTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKR
TTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSG
ASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESH
QKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNAAFPPLER
KPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKC
YMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTT
PYEPKRGLPL

3D structure

• PDB: 8f5w Mammalian dihydropyrimidine dehydrogenase: Added mechanistic details from transient-state analysis of charge transfer complexes.
• Chain: A
• Resolution: 1.97 Å

Enzymatic activity

• Enzyme Commision number: 1.3.1.2: dihydropyrimidine dehydrogenase (NADP(+)).

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	SF4	A	I948 C953 I954 N955 C956 G957 C959 P980 C996 P997 C1001 I1002	I939 C944 I945 N946 C947 G948 C950 P971 C987 P988 C992 I993
BS02	SF4	A	C963 Y968 I971 C986 T987 G988 C989 T990 C992	C954 Y959 I962 C977 T978 G979 C980 T981 C983
BS03	SF4	A	C79 L80 K81 C82 P86 C87 C140 N141 L142 I150 I152	C77 L78 K79 C80 P84 C85 C138 N139 L140 I148 I150
BS04	SF4	A	C91 L95 I97 C130 C136 Q156	C89 L93 I95 C128 C134 Q154
BS05	FAD	A	V129 G194 G196 P197 A198 E218 K219 G225 L226 E230 I231 R235 S260 L261 I283 T343 G480 D481 T488 T489 S492	V127 G192 G194 P195 A196 E216 K217 G223 L224 E228 I229 R233 S258 L259 I281 T341 G478 D479 T486 T487 S490
BS06	NAP	A	P131 A340 G341 D342 T343 R364 K365 R371 F438 G439 N487	P129 A338 G339 D340 T341 R362 K363 R369 F436 G437 N485
BS07	FNR	A	S550 A551 A552 K574 T575 N609 N668 K709 N736 S766 G767 T793 G794 G795 C816 S817	S548 A549 A550 K572 T573 N607 N666 K700 N727 S757 G758 T784 G785 G786 C807 S808
BS08	TDR	A	N609 N736 T737	N607 N727 T728

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0002058 uracil binding
• GO:0010181 FMN binding
• GO:0016491 oxidoreductase activity
• GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
• GO:0017113 dihydropyrimidine dehydrogenase (NADP+) activity
• GO:0042803 protein homodimerization activity
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0050661 NADP binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006210 thymine catabolic process
• GO:0006212 uracil catabolic process
• GO:0006214 thymidine catabolic process
• GO:0019483 beta-alanine biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:8f5w, PDBe:8f5w, PDBj:8f5w
• PDBsum: 8f5w
• PubMed: 36681231
• UniProt: Q28943|DPYD_PIG Dihydropyrimidine dehydrogenase [NADP(+)] (Gene Name=DPYD)