2rcy

Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound

Method: X-RAY DIFFRACTION

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

Pyrroline carboxylate reductase

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	MAGNESIUM ION × 8 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 10 GLYCEROL × 4 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8IDC6_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–262； UniProt 1–261 Author chain B； PDBConstruct 2–262； UniProt 1–261 Author chain C； PDBConstruct 2–262； UniProt 1–261 Author chain D； PDBConstruct 2–262； UniProt 1–261 Author chain E； PDBConstruct 2–262； UniProt 1–261

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	2rcy
Deposition date deposition_date	2007-09-20
Structure title title	Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound
Keywords keywords	malaria, structural genomics, pyrroline reductase, Oxidoreductase, Structural Genomics Consortium, SGC; 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.

2rcy__assembly_1__model_1

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

Download this curve (.dat)

2rcy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2rcy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.82 Å
Rg (electron density)	40.98 Å
Total Rg	41.23 Å
Atom count	19304
Residues	2442
Excluded volume	346880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2rcy__assembly_1__model_1`	decameric （10）	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	Pyrroline carboxylate reductase
Molecular weight formula_weight	28806.8 kDa
EC 编号 ec_number	1.5.1.2
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	10098

GMENIKLGFMGLGQMGSALAHGIANANIIKKENLFYYGPSKKNTTLNYMSSNEELARHCDIIVCAVKPDIAGSVLNNIKPYLSSKLLISICGGLNIGKLEEMVGSENKIVWVMPNTPCLVGEGSFIYCSNKNVNSTDKKYVNDIFNSCGIIHEIKEKDMDIATAISGCGPAYVYLFIESLIDAGVKNGLSRELSKNLVLQTIKGSVEMVKKSDQPVQQLKDNIVSPGGITAVGLYSLEKNSFKYTVMNAVEAACEKSKAMGS

Source Source

Source organism organism	Plasmodium falciparum
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	5

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	427

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6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d2rcya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2rcya2
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.0 — automated matches

Domain ID domain_id	d2rcya3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2rcyb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2rcyb2
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.0 — automated matches

Domain ID domain_id	d2rcyc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2rcyc2
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.0 — automated matches

Domain ID domain_id	d2rcyd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2rcyd2
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.0 — automated matches

Domain ID domain_id	d2rcye1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2rcye2
Class class	a — All alpha proteins
Fold Fold fold	a.100 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Superfamily Superfamily superfamily	a.100.1 — 6-phosphogluconate dehydrogenase C-terminal domain-like
Family Family family	a.100.1.0 — automated matches

CATH v4.4 (10 domains)

Domain ID domain_id	2rcyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2rcyA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3730 — ProC C-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — ProC C-terminal domain-like

Domain ID domain_id	2rcyB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2rcyB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3730 — ProC C-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — ProC C-terminal domain-like

Domain ID domain_id	2rcyC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2rcyC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3730 — ProC C-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — ProC C-terminal domain-like

Domain ID domain_id	2rcyD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2rcyD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3730 — ProC C-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — ProC C-terminal domain-like

Domain ID domain_id	2rcyE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2rcyE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3730 — ProC C-terminal domain-like fold
Homologous superfamily homologous superfamily	10 — ProC C-terminal domain-like

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Unit-cell length a length_a	160.207 Å
Unit-cell length b length_b	113.741 Å
Unit-cell length c length_c	82.651 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.270 Å
R factor r_factor	0.2470
R_work r_work	0.2450
R_free r_free	0.2890

Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound

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

Pyrroline carboxylate 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

2rcy__assembly_1__model_1

2rcy__assembly_1__model_1 | I(q)

2rcy__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

6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (11 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of Plasmodium falciparum pyrroline carboxylate reductase (MAL13P1.284) with NADP bound

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

Pyrroline carboxylate 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

2rcy__assembly_1__model_1

2rcy__assembly_1__model_1 | I(q)

2rcy__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

6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (11 domains)

CATH v4.4 (10 domains)

7. Citations (1)