13pk

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI

Method: X-RAY DIFFRACTION

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

3-PHOSPHOGLYCERATE KINASE

Trypanosoma brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 PHOSPHATE ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 3-PHOSPHOGLYCERIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 3-PHOSPHOGLYCERIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 PHOSPHATE ION × 3 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 PHOSPHATE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PGKC_TRYBB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–415； UniProt 5–419 Author chain B； PDBConstruct 1–415； UniProt 5–419 Author chain C； PDBConstruct 1–415； UniProt 5–419 Author chain D； PDBConstruct 1–415； UniProt 5–419

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	13pk
Deposition date deposition_date	1996-11-23
Structure title title	TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI
Keywords keywords	KINASE, PHOSPHOGLYCERATE, TERNARY COMPLEX, GLYCOLYSIS, TRANSFERASE; KINASE
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.

13pk__assembly_4__model_1

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

Download this curve (.dat)

13pk__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

13pk__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	22.73 Å
Rg (electron density)	21.97 Å
Total Rg	22.75 Å
Atom count	3160
Residues	415
Excluded volume	56831 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`13pk__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`13pk__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`13pk__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`13pk__assembly_4__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	3-PHOSPHOGLYCERATE KINASE
Molecular weight formula_weight	44700.0 kDa
EC 编号 ec_number	2.7.2.3
Mutation mutation	TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE
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	13271

EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEGGSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKRLSELLLRPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYSIGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITEDQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTFAIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLELLEGKTLPGVTVLDDK

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
Host organism host_organism	Escherichia coli BL21

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	3-PHOSPHOGLYCERIC ACID
Molecular weight formula_weight	186.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	599

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d13pka_
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	d13pkb_
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	d13pkc_
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	d13pkd_
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

CATH v4.4 (8 domains)

Domain ID domain_id	13pkA01
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	13pkA02
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	13pkB01
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	13pkB02
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	13pkC01
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	13pkC02
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	13pkD01
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	13pkD02
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	113.213 Å
Unit-cell length b length_b	115.959 Å
Unit-cell length c length_c	171.327 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2206
R_work r_work	0.2206
R_free r_free	0.2910

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI

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

3-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

13pk__assembly_4__model_1

13pk__assembly_4__model_1 | I(q)

13pk__assembly_4__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI

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

3-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

13pk__assembly_4__model_1

13pk__assembly_4__model_1 | I(q)

13pk__assembly_4__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)