2azn

X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase

Method: X-RAY DIFFRACTION

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

Putative 5-amino-6-(5-phosphoribosylamino)uracil reductase

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 1 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 2 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 2 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 1 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 2 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 4 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 1 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ; × 3 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIB7_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–219； UniProt 6–224 Author chain B； PDBConstruct 1–219； UniProt 6–224 Author chain C； PDBConstruct 1–219； UniProt 6–224 Author chain D； PDBConstruct 1–219； UniProt 6–224 Author chain E； PDBConstruct 1–219； UniProt 6–224 Author chain F； PDBConstruct 1–219； UniProt 6–224

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	2azn
Deposition date deposition_date	2005-09-12
Structure title title	X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase
Keywords keywords	OXIDOREDUCTASE; 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.

2azn__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2azn__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2azn__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.51 Å
Rg (electron density)	17.68 Å
Total Rg	18.62 Å
Atom count	1789
Residues	214
Excluded volume	32383 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2azn__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2azn__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2azn__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2azn__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2azn__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2azn__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2azn__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2azn__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2azn__assembly_9__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 (5)

Entity 1 Entity 1 polymer

Description description	Putative 5-amino-6-(5-phosphoribosylamino)uracil reductase
Molecular weight formula_weight	24721.2 kDa
EC 编号 ec_number	1.1.1.193
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	11090

EKKPYIISNVGMTLDGKLATINNDSRISCEEDLIRVHKIRANVDGIMVGIGTVLKDDPRLTVHKIKSDRNPVRIVVDSKLRVPLNARVLNKDAKTIIATTEDTNEEKEKKIKILEDMGVEVVKCGRGKVDLKKLMDILYDKGIKSILLEGGGTLNWGMFKEGLVDEVSVYIAPKIFGGKEAPTYVDGEGFKTVDECVKLELKNFYRLGEGIVLEFKVKK

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;2-(6-(2-CYCLOHEXYLETHOXY)-TETRAHYDRO-4,5-DIHYDROXY-2(HYDROXYMETHYL)-2H-PYRAN-3-YLOXY)-TETRAHYDRO-6(HYDROXYMETHYL)-2H-PY RAN-3,4,5-TRIOL ;
Molecular weight formula_weight	452.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 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	6

Entity 4 Entity 4 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2azna1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.2 — RibD C-terminal domain-like

Domain ID domain_id	d2aznb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.2 — RibD C-terminal domain-like

Domain ID domain_id	d2aznc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.2 — RibD C-terminal domain-like

Domain ID domain_id	d2aznd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.2 — RibD C-terminal domain-like

Domain ID domain_id	d2azne_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.2 — RibD C-terminal domain-like

Domain ID domain_id	d2aznf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.71 — Dihydrofolate reductase-like
Superfamily Superfamily superfamily	c.71.1 — Dihydrofolate reductase-like
Family Family family	c.71.1.2 — RibD C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id	2aznA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	2aznB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	2aznC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	2aznD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	2aznE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

Domain ID domain_id	2aznF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	430 — Dihydrofolate Reductase, subunit A
Homologous superfamily homologous superfamily	10 — Dihydrofolate Reductase, subunit A

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Unit-cell length a length_a	137.171 Å
Unit-cell length b length_b	137.171 Å
Unit-cell length c length_c	213.870 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2300
R_work r_work	0.2300
R_free r_free	0.2530

X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase

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

Putative 5-amino-6-(5-phosphoribosylamino)uracil reductase

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

2azn__assembly_4__model_1

2azn__assembly_4__model_1 | I(q)

2azn__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

X-RAY Structure of 2,5-diamino-6-ribosylamino-4(3h)-pyrimidinone 5-phosphate reductase

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

Putative 5-amino-6-(5-phosphoribosylamino)uracil reductase

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

2azn__assembly_4__model_1

2azn__assembly_4__model_1 | I(q)

2azn__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)