6qu5

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12

Method: X-RAY DIFFRACTION

▼

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

ATP-dependent 6-phosphofructokinase

Trypanosoma brucei brucei

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CITRIC ACID × 4 GLYCEROL × 2 1-[(3,4-dichlorophenyl)methyl]imidazole × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CITRIC ACID × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PFKA_TRYBB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–507； UniProt 1–487 Author chain B； PDBConstruct 21–507； UniProt 1–487 Author chain C； PDBConstruct 21–507； UniProt 1–487 Author chain D； PDBConstruct 21–507； UniProt 1–487 Author chain E； PDBConstruct 21–507； UniProt 1–487 Author chain F； PDBConstruct 21–507； UniProt 1–487 Author chain G； PDBConstruct 21–507； UniProt 1–487 Author chain H； PDBConstruct 21–507； UniProt 1–487

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6qu5
Deposition date deposition_date	2019-02-26
Structure title title	Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12
Keywords keywords	Glycolysis, Inhibitor, Allostery, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6qu5__assembly_1__model_1

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

Download this curve (.dat)

6qu5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qu5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.92 Å
Rg (electron density)	34.82 Å
Total Rg	35.45 Å
Atom count	14163
Residues	1825
Excluded volume	252040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qu5__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6qu5__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ATP-dependent 6-phosphofructokinase
Molecular weight formula_weight	55764.7 kDa
EC 编号 ec_number	2.7.1.11
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	28255

MGSSHHHHHHSSGLVPRGSHMAVESRSRVTSKLVKAHRAMLNSVTQEDLKVDRLPGADYPNPSKKYSSRTEFRDKTDYIMYNPRPRDEPSSENPVSVSPLLCELAAARSRIHFNPTETTIGIVTCGGICPGLNDVIRSITLTGINVYNVKRVIGFRFGYWGLSKKGSQTAIELHRGRVTNIHHYGGTILGSSRGPQDPKEMVDTLERLGVNILFTVGGDGTQRGALVISQEAKRRGVDISVFGVPKTIDNDLSFSHRTFGFQTAVEKAVQAIRAAYAEAVSANYGVGVVKLMGRDSGFIAAQAAVASAQANICLVPENPISEQEVMSLLERRFCHSRSCVIIVAEGFGQDWGRGSGGYDASGNKKLIDIGVILTEKVKAFLKANKSRYPDSTVKYIDPSYMIRACPPSANDALFCATLATLAVHEAMAGATGCIIAMRHNNYILVPIKVATSVRRVLDLRGQLWRQVREITVDLGSDVRLARKLEIRRELEAINRNRDRLHEELAKL

Source Source

Source organism organism	Trypanosoma brucei brucei
NCBI taxonomy ID ncbi_taxonomy_id	5702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	8

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 non-polymer

Description description	1-[(3,4-dichlorophenyl)methyl]imidazole
Molecular weight formula_weight	227.1 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	6qu5A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5B03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5C03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5D03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5E02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5E03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5F02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5F03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5G02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5G03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

Domain ID domain_id	6qu5H02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	450 —

Domain ID domain_id	6qu5H03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	460 — Phosphofructokinase domain

▶

Unit-cell length a length_a	115.251 Å
Unit-cell length b length_b	132.513 Å
Unit-cell length c length_c	282.699 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	32

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

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	96.670 Å
R factor r_factor	0.2505
R_work r_work	0.2497
R_free r_free	0.2671

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12

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

ATP-dependent 6-phosphofructokinase

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

6qu5__assembly_1__model_1

6qu5__assembly_1__model_1 | I(q)

6qu5__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 (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 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

Crystal Structure of Phosphofructokinase from Trypanosoma brucei in complex with an allosteric inhibitor ctcb12

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

ATP-dependent 6-phosphofructokinase

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

6qu5__assembly_1__model_1

6qu5__assembly_1__model_1 | I(q)

6qu5__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 (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 non-polymer

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)