8f61

Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Dihydrothymine Quasi-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 THYMINE × 1 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 × 1 FLAVIN MONONUCLEOTIDE × 1 (5S)-5-methyl-1,3-diazinane-2,4-dione × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	IRON/SULFUR CLUSTER × 8 FLAVIN-ADENINE DINUCLEOTIDE × 2 THYMINE × 1 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 × 1 FLAVIN MONONUCLEOTIDE × 1 (5S)-5-methyl-1,3-diazinane-2,4-dione × 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	8f61
Deposition date deposition_date	2022-11-15
Structure title title	Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Dihydrothymine Quasi-Anaerobically
Keywords keywords	dihydropyrimidine dehydrogenase, dehydrogenase, mutant, dihydrothymine, flavoprotein; FLAVOPROTEIN
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.

8f61__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8f61__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8f61__assembly_2__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)	37.22 Å
Total Rg	37.30 Å
Atom count	15711
Residues	2032
Excluded volume	281480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8f61__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8f61__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 (8)

Entity 1 Entity 1 polymer

Description description	Dihydropyrimidine dehydrogenase [NADP(+)]
Molecular weight formula_weight	111587.3 kDa
EC 编号 ec_number	1.3.1.2
Mutation mutation	C671S
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	32219

MAPVLSKDVADIESILALNPRTQSHAALHSTLAKKLDKKHWKRNPDKNCFHCEKLENNFDDIKHTTLGERGALREAMRCLKCADAPCQKSCPTHLDIKSFITSISNKNYYGAAKMIFSDNPLGLTCGMVCPTSDLCVGGCNLYATEEGSINIGGLQQFASEVFKAMNIPQIRNPCLPSQEKMPEAYSAKIALLGAGPASISCASFLARLGYSDITIFEKQEYVGGLSTSEIPQFRLPYDVVNFEIELMKDLGVKIICGKSLSENEITLNTLKEEGYKAAFIGIGLPEPKTDDIFQGLTQDQGFYTSKDFLPLVAKSSKAGMCACHSPLPSIRGAVIVLGAGDTAFDCATSALRCGARRVFLVFRKGFVNIRAVPEEVELAKEEKCEFLPFLSPRKVIVKGGRIVAVQFVRTEQDETGKWNEDEDQIVHLKADVVISAFGSVLRDPKVKEALSPIKFNRWDLPEVDPETMQTSEPWVFAGGDIVGMANTTVESVNDGKQASWYIHKYIQAQYGASVSAKPELPLFYTPVDLVDISVEMAGLKFINPFGLASAAPTTSSSMIRRAFEAGWGFALTKTFSLDKDIVTNVSPRIVRGTTSGPMYGPGQSSFLNIELISEKTAAYWCQSVTELKADFPDNIVIASIMCSYNKNDWMELSRKAEASGADALELNLSSPHGMGERGMGLACGQDPELVRNICRWVRQAVQIPFFAKLTPNVTDIVSIARAAKEGGADGVTATNTVSGLMGLKADGTPWPAVGAGKRTTYGGVSGTAIRPIALRAVTTIARALPGFPILATGGIDSAESGLQFLHSGASVLQVCSAVQNQDFTVIQDYCTGLKALLYLKSIEELQGWDGQSPGTESHQKGKPVPRIAELMGKKLPNFGPYLEQRKKIIAEEKMRLKEQNAAFPPLERKPFIPKKPIPAIKDVIGKALQYLGTFGELSNIEQVVAVIDEEMCINCGKCYMTCNDSGYQAIQFDPETHLPTVTDTCTGCTLCLSVCPIIDCIRMVSRTTPYEPKRGLPLAVNPVC

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	THYMINE
Molecular weight formula_weight	126.1 kDa
Source method src_method	syn
Copy count entity_count	2

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	2

Entity 6 Entity 6 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	(5S)-5-methyl-1,3-diazinane-2,4-dione
Molecular weight formula_weight	128.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	797

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8f61A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	8f61B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	8f61C01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	8f61D01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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Unit-cell length a length_a	81.784 Å
Unit-cell length b length_b	157.667 Å
Unit-cell length c length_c	162.564 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.93 °
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	2.140 Å
Low-resolution limit resolution_low	161.690 Å
R factor r_factor	0.1891
R_work r_work	0.1870
R_free r_free	0.2298

Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Dihydrothymine Quasi-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

8f61__assembly_2__model_1

8f61__assembly_2__model_1 | I(q)

8f61__assembly_2__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Dihydrothymine Quasi-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

8f61__assembly_2__model_1

8f61__assembly_2__model_1 | I(q)

8f61__assembly_2__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 (8)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)