SAXSdb — 3oza

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

Phosphoglycerate kinase

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	SULFATE ION × 3 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGK_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–424； UniProt 2–416 Author chain B； PDBConstruct 10–424； UniProt 2–416 Author chain C； PDBConstruct 10–424； UniProt 2–416

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	3oza
Deposition date deposition_date	2010-09-24
Structure title title	Crystal Structure of Plasmodium falciparum 3-Phosphoglycerate Kinase
Keywords keywords	Phosphoglycerate Kinase, Transferase, Kinase, Nucleotide binding, ATP binding, Glycolysis, Malaraia Parasite; TRANSFERASE
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.

3oza__assembly_2__model_1

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

Download this curve (.dat)

3oza__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3oza__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.63 Å
Rg (electron density)	27.69 Å
Total Rg	28.52 Å
Atom count	6536
Residues	830
Excluded volume	117490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3oza__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3oza__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 (4)

Entity 1 Entity 1 polymer

Description description	Phosphoglycerate kinase
Molecular weight formula_weight	46965.6 kDa
EC 编号 ec_number	2.7.2.3
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9714

HSMHHHHHHLGNKLSISDLKDIKNKKVLVRVDFNVPIENGIIKDTNRITATLPTINHLKKEGASKIILISHCGRPDGLRNEKYTLKPVAETLKGLLGEEVLFLNDCVGKEVEDKINAAKENSVILLENLRFHIEEEGKGVDANGNKVKANKEDVEKFQNDLTKLADVFINDAFGTAHRAHSSMVGVKLNVKASGFLMKKELEYFSKALENPQRPLLAILGGAKVSDKIQLIKNLLDKVDRMIIGGGMAYTFKKVLNNMKIGTSLFDEAGSKIVGEIMEKAKAKNVQIFLPVDFKIADNFDNNANTKFVTDEEGIPDNWMGLDAGPKSIENYKDVILTSKTVIWNGPQGVFEMPNFAKGSIECLNLVVEVTKKGAITIVGGGDTASLVEQQNKKNEISHVSTGGGASLELLEGKELPGVLALSNK

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	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	46

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3ozaa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.86 — Phosphoglycerate kinase
Superfamily Superfamily superfamily	c.86.1 — Phosphoglycerate kinase
Family Family family	c.86.1.1 — Phosphoglycerate kinase

Domain ID domain_id	d3ozaa2
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	d3ozab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.86 — Phosphoglycerate kinase
Superfamily Superfamily superfamily	c.86.1 — Phosphoglycerate kinase
Family Family family	c.86.1.1 — Phosphoglycerate kinase

Domain ID domain_id	d3ozab2
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	d3ozac1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.86 — Phosphoglycerate kinase
Superfamily Superfamily superfamily	c.86.1 — Phosphoglycerate kinase
Family Family family	c.86.1.1 — Phosphoglycerate kinase

Domain ID domain_id	d3ozac2
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

CATH v4.4 (6 domains)

Domain ID domain_id	3ozaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1260 — Phosphoglycerate kinase, N-terminal domain

Domain ID domain_id	3ozaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1260 — Phosphoglycerate kinase, N-terminal domain

Domain ID domain_id	3ozaB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1260 — Phosphoglycerate kinase, N-terminal domain

Domain ID domain_id	3ozaB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1260 — Phosphoglycerate kinase, N-terminal domain

Domain ID domain_id	3ozaC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1260 — Phosphoglycerate kinase, N-terminal domain

Domain ID domain_id	3ozaC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1260 — Phosphoglycerate kinase, N-terminal domain

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Unit-cell length a length_a	119.030 Å
Unit-cell length b length_b	147.610 Å
Unit-cell length c length_c	206.490 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	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.2072
R_work r_work	0.2003
R_free r_free	0.2714

Crystal Structure of Plasmodium falciparum 3-Phosphoglycerate Kinase

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

Phosphoglycerate kinase

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

3oza__assembly_2__model_1

3oza__assembly_2__model_1 | I(q)

3oza__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Plasmodium falciparum 3-Phosphoglycerate Kinase

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

Phosphoglycerate kinase

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

3oza__assembly_2__model_1

3oza__assembly_2__model_1 | I(q)

3oza__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)