SAXSdb — 9kp9

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

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MANGANESE (II) ION × 2 [(~{S})-(3-hexoxyphenyl)-[2-[methyl(oxidanyl)amino]-2-oxidanylidene-ethyl]sulfanyl-methyl]phosphonic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DXR_PLAFX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–488； UniProt 1–488

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	9kp9
Deposition date deposition_date	2024-11-22
Last revision last_revision	2025-05-21
Structure title title	PfDXR - Mn2+ - NADPH - TAKK443 quaternary complex
Keywords keywords	Inhibitor, Malaria, ISOMERASE; ISOMERASE
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.

9kp9__assembly_1__model_1

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

Download this curve (.dat)

9kp9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9kp9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.22 Å
Rg (electron density)	30.66 Å
Total Rg	31.20 Å
Atom count	6718
Residues	822
Excluded volume	120670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9kp9__assembly_1__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	1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
Molecular weight formula_weight	55829.6 kDa
EC 编号 ec_number	1.1.1.267
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3557

MKKYIYIYFFFITITINDLVINNTSKCVSIERRKNNAYINYGIGYNGPDNKITKSRRCKRIKLCKKDLIDIGAIKKPINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHNSS

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	[(~{S})-(3-hexoxyphenyl)-[2-[methyl(oxidanyl)amino]-2-oxidanylidene-ethyl]sulfanyl-methyl]phosphonic acid
Molecular weight formula_weight	391.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	198

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Unit-cell length a length_a	92.498 Å
Unit-cell length b length_b	92.498 Å
Unit-cell length c length_c	105.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	80.110 Å
R factor r_factor	0.1684
R_work r_work	0.1664
R_free r_free	0.2056

PfDXR - Mn2+ - NADPH - TAKK443 quaternary complex

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

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic

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

9kp9__assembly_1__model_1

9kp9__assembly_1__model_1 | I(q)

9kp9__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 (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

7. Citations (1)

PfDXR - Mn2+ - NADPH - TAKK443 quaternary complex

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

1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic

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

9kp9__assembly_1__model_1

9kp9__assembly_1__model_1 | I(q)

9kp9__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 (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

7. Citations (1)