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16pk

PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG

Method: X-RAY DIFFRACTION Dmax: 73.7 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

3-PHOSPHOGLYCERATE KINASE

Trypanosoma brucei

UniProt P07378

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 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

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 16PK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
13PK TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI Deposited 1996-11-23 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 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
13PK TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI Deposited 1996-11-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 5–419（415 aa）
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
13PK TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI Deposited 1996-11-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 5–419（415 aa）
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
13PK TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI Deposited 1996-11-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 5–419（415 aa）
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

1 other PDB entries and 4 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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 16pk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 16pk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id16pk
Deposition date deposition_date1998-05-18
Structure title titlePHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG
Keywords keywordsKINASE, PHOSPHOGLYCERATE, TERNARY COMPLEX, GLYCOLYSIS, TRANSFERASE, BISUBSTRATE, ANALOG; KINASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.76 Å
Radius of gyration Rg (electron density) rg_electron23.05 Å
Forward intensity I(0) i034436700.00
Molecular weight molecular_weight45519.0 kDa
Excluded volume excluded_volume57246 ų
Envelope volume envelope_volume67299 ų
Hydration-shell volume shell_volume24502 ų
Envelope diameter envelope_diameter76.6 Å
Shell Rg shell_rg29.82 Å
Envelope Rg envelope_rg23.02 Å
Shape Rg shape_rg23.05 Å
Total Rg total_rg23.84 Å
Total atoms total_atoms3189
Residues n_residues415
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.7 Å
Rg (real space) rg_real23.74 Å
Rg uncertainty (real space) rg_real_error0.44 Å
I(0) (real space) i0_real3.4440e+07
I(0) uncertainty (real space) i0_real_error4.8650e+05
Rg (reciprocal space) rg_reciprocal23.74 Å
I(0) (reciprocal space) i0_reciprocal34440000.0000
Solution quality estimate total_estimate0.9014
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.5 Å
Skewness Skewness skewness0.317
Kurtosis Kurtosis kurtosis-0.470
Angular range angular_range— – 0.3350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6450000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.891
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd16pka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.86 — Phosphoglycerate kinase
Superfamily Superfamily superfamilyc.86.1 — Phosphoglycerate kinase
Family Family familyc.86.1.1 — Phosphoglycerate kinase

CATH v4.4 (2 domains)

Domain ID domain_id16pkA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1260 — Phosphoglycerate kinase, N-terminal domain
Domain ID domain_id16pkA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1260 — Phosphoglycerate kinase, N-terminal domain
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8. Citations (1)

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9. Files and Curves (10)