7m32

Dihydropyrimidine Dehydrogenase (DPD) C671A Mutant Soaked with Uracil and NADPH Anaerobically

Method: X-RAY DIFFRACTION

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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 URACIL × 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 ALANINE × 1 LEUCINE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	IRON/SULFUR CLUSTER × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 URACIL × 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 ALANINE × 1 LEUCINE × 1 PROLINE × 1 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7m32
Deposition date deposition_date	2021-03-18
Structure title title	Dihydropyrimidine Dehydrogenase (DPD) C671A Mutant Soaked with Uracil and NADPH Anaerobically
Keywords keywords	Dihydropyrimidine Dehydrogenase, DPD, mutant, uracil, flavin, soaking, ligand, FMN, FAD, FLAVOPROTEIN, Oxidoreductase; FLAVOPROTEIN, Oxidoreductase
Experimental Method method	X-RAY DIFFRACTION

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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.

7m32__assembly_1__model_1

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

Download this curve (.dat)

7m32__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7m32__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.57 Å
Rg (electron density)	37.26 Å
Total Rg	37.31 Å
Atom count	15589
Residues	2021
Excluded volume	279480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7m32__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7m32__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Dihydropyrimidine dehydrogenase [NADP(+)]
Molecular weight formula_weight	111571.3 kDa
EC 编号 ec_number	1.3.1.2
Mutation mutation	C671A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	33840

MAPVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHCEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFITSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINIGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISCASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLGVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQGFYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSALRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSPIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAPTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMELSRKAEASGADALELNLSAPHGMGERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNAAFPPLERKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGLPLAVNPVC

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	URACIL
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	ALANINE
Molecular weight formula_weight	89.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	LEUCINE
Molecular weight formula_weight	131.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 non-polymer

Description description	PROLINE
Molecular weight formula_weight	115.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2630

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

Domain ID domain_id	d7m32a1
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	d7m32a2
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	d7m32a3
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	d7m32a4
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	d7m32a5
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	d7m32b1
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	d7m32b2
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	d7m32b3
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	d7m32b4
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	d7m32b5
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	d7m32c1
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	d7m32c2
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	d7m32c3
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	d7m32c4
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	d7m32c5
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	d7m32d1
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	d7m32d2
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	d7m32d3
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	d7m32d4
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	d7m32d5
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

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Unit-cell length a length_a	81.870 Å
Unit-cell length b length_b	158.730 Å
Unit-cell length c length_c	162.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.89 °
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	1.820 Å
Low-resolution limit resolution_low	47.260 Å
R factor r_factor	0.1706
R_work r_work	0.1689
R_free r_free	0.2019

Dihydropyrimidine Dehydrogenase (DPD) C671A Mutant Soaked with Uracil and NADPH Anaerobically

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

7m32__assembly_1__model_1

7m32__assembly_1__model_1 | I(q)

7m32__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 (9)

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

7. Citations (1)

Dihydropyrimidine Dehydrogenase (DPD) C671A Mutant Soaked with Uracil and NADPH Anaerobically

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

7m32__assembly_1__model_1

7m32__assembly_1__model_1 | I(q)

7m32__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 (9)

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 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (20 domains)

7. Citations (1)