7lju

Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU)

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydropyrimidine dehydrogenase [NADP(+)]

Sus scrofa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	IRON/SULFUR CLUSTER × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-ethynylpyrimidine-2,4(1H,3H)-dione × 2 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	IRON/SULFUR CLUSTER × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 5-ethynylpyrimidine-2,4(1H,3H)-dione × 2 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPYD_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1025； UniProt 1–1025 Author chain B； PDBConstruct 1–1025； UniProt 1–1025 Author chain C； PDBConstruct 1–1025； UniProt 1–1025 Author chain D； PDBConstruct 1–1025； UniProt 1–1025

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7lju
Deposition date deposition_date	2021-01-30
Structure title title	Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU)
Keywords keywords	Dihydropyrimidine dehydrogenase, DPD, dehydrogenase, 5-Ethynyluracil, 5EU, inhibitor, inactivator, crosslinking, FLAVOPROTEIN; FLAVOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7lju__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7lju__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7lju__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.54 Å
Rg (electron density)	37.22 Å
Total Rg	37.28 Å
Atom count	15731
Residues	2020
Excluded volume	281490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7lju__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7lju__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Dihydropyrimidine dehydrogenase [NADP(+)]
Molecular weight formula_weight	111603.3 kDa
EC 编号 ec_number	1.3.1.2
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,D,B
Atom count atom_count	34870

MAPVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHCEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFITSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINIGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISCASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLGVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQGFYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSALRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSPIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAPTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMELSRKAEASGADALELNLSCPHGMGERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNAAFPPLERKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGLPLAVNPVC

Source Source

Source organism organism	Sus scrofa
Common name common_name	Pig
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	16

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	5-ethynylpyrimidine-2,4(1H,3H)-dione
Molecular weight formula_weight	136.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
Molecular weight formula_weight	458.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3389

▼

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d7ljua1
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.2 — alpha-helical ferredoxin
Family Family family	a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain

Domain ID domain_id	d7ljua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljua3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljua4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d7ljua5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d7ljub1
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.2 — alpha-helical ferredoxin
Family Family family	a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain

Domain ID domain_id	d7ljub2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljub3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljub4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d7ljub5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d7ljuc1
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.2 — alpha-helical ferredoxin
Family Family family	a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain

Domain ID domain_id	d7ljuc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljuc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljuc4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d7ljuc5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

Domain ID domain_id	d7ljud1
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.2 — alpha-helical ferredoxin
Family Family family	a.1.2.2 — Dihydropyrimidine dehydrogenase, N-terminal domain

Domain ID domain_id	d7ljud2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.4 — Nucleotide-binding domain
Superfamily Superfamily superfamily	c.4.1 — Nucleotide-binding domain
Family Family family	c.4.1.1 — N-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljud3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamily	c.3.1 — FAD/NAD(P)-binding domain
Family Family family	c.3.1.1 — C-terminal domain of adrenodoxin reductase-like

Domain ID domain_id	d7ljud4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

Domain ID domain_id	d7ljud5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.1 — 4Fe-4S ferredoxins
Family Family family	d.58.1.5 — Ferredoxin domains from multidomain proteins

▶

Unit-cell length a length_a	82.060 Å
Unit-cell length b length_b	158.940 Å
Unit-cell length c length_c	163.210 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	40.590 Å
R factor r_factor	0.1739
R_work r_work	0.1719
R_free r_free	0.2109

Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydropyrimidine dehydrogenase [NADP(+)]

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7lju__assembly_1__model_1

7lju__assembly_1__model_1 | I(q)

7lju__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

7. Citations (1)

Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydropyrimidine dehydrogenase [NADP(+)]

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7lju__assembly_1__model_1

7lju__assembly_1__model_1 | I(q)

7lju__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

7. Citations (1)