SAXSdb — 13pk

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 5–419	Mutation：TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 3PG 3-PHOSPHOGLYCERIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion	Resolution 2.50 Å R-free 0.291
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 5–419	Mutation：TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 3PG 3-PHOSPHOGLYCERIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion	Resolution 2.50 Å R-free 0.291
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 5–419	Mutation：TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion	Resolution 2.50 Å R-free 0.291
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 5–419	Mutation：TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion	Resolution 2.50 Å R-free 0.291

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 13PK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
16PK PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG Deposited 1998-05-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–419（415 aa）	Mutation：TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE	BIS 1,1,5,5-TETRAFLUOROPHOSPHOPENTYLPHOSPHONIC ACID ADENYLATE ESTER × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.7；VAPOR DIFFUSION BY MIXING, pH 7.7, vapor diffusion	Resolution 1.60 Å R-free 0.235

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	41.75 Å
Radius of gyration Rg (electron density) rg_electron	41.63 Å
Forward intensity I(0) i0	484053000.00
Molecular weight molecular_weight	181340.0 kDa
Excluded volume excluded_volume	227720 Å³
Envelope volume envelope_volume	283910 Å³
Hydration-shell volume shell_volume	57592 Å³
Envelope diameter envelope_diameter	145.7 Å
Shell Rg shell_rg	46.39 Å
Envelope Rg envelope_rg	41.10 Å
Shape Rg shape_rg	41.64 Å
Total Rg total_rg	41.83 Å
Total atoms total_atoms	12672
Residues n_residues	1660
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	139.9 Å
Rg (real space) rg_real	41.88 Å
Rg uncertainty (real space) rg_real_error	1.24 Å
I(0) (real space) i0_real	4.8410e+08
I(0) uncertainty (real space) i0_real_error	8.5190e+06
Rg (reciprocal space) rg_reciprocal	41.75 Å
I(0) (reciprocal space) i0_reciprocal	484000000.0000
Solution quality estimate total_estimate	0.8720
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.2 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.458
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	50620000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.772

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Trypanosoma brucei
NCBI Class编号 ncbi_taxonomy_id	5691
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/3p/13pk/13pk.fit
pddf	/app/data/pr_computation/3p/13pk/13pk.pr.out
profile	/app/data/saxs_computation/3p/13pk/13pk.dat

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI