SAXSdb — 5brd

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

Glucokinase 1, putative

Trypanosoma cruzi (strain CL Brener)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-(benzoylamino)-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4E4E1_TRYCC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–381； UniProt 1–367 Author chain B； PDBConstruct 15–381； UniProt 1–367

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	5brd
Deposition date deposition_date	2015-05-30
Structure title title	Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN
Keywords keywords	Transferase, Hexose Kinase, Transferase-Transferase Inhibitor complex; Transferase/Transferase Inhibitor
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.

5brd__assembly_1__model_1

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

Download this curve (.dat)

5brd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5brd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.96 Å
Rg (electron density)	27.05 Å
Total Rg	27.87 Å
Atom count	5736
Residues	734
Excluded volume	102480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5brd__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Glucokinase 1, putative
Molecular weight formula_weight	42226.6 kDa
EC 编号 ec_number	2.7.1.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5823

MGRGSHHHHHHGMAMNIKELSLHELCEELKTPAWNVPLTFVGDVGGTSARMGFVREGKNDSVHACVTRYSMKRKDITELIEFFNEIIELMPASVIKRVKAGVINVPGPVTGGAVGGPFNNLKGIARLSDYPKALFPPGRSAILNDLEAGGFGVLAVSDAHVFSEYFGVMWEGTQWRTCEQEPAGSVIGRGRCLVLAPGTGLGSSLIYYNPMNQQHIVVPLELGSQTIPMRKDIDYIQTLHAELKLLPNYENMVSGAGLEFHYRQVVRGSRPPCSAGEIAKLASEGDANACKAMKKYHEYLMRVGSEASMALLPLTIVLVGDNIVNNAFFYRNPQNLKEMHREALNHEMERFGFQSRVTYLRQKKLLNLNLMGCYRCGLDLS

Source Source

Source organism organism	Trypanosoma cruzi (strain CL Brener)
NCBI taxonomy ID ncbi_taxonomy_id	353153
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-(benzoylamino)-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	283.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	87

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5brdA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	5brdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	5brdB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	5brdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	367 — Hexokinase; domain 1
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	68.567 Å
Unit-cell length b length_b	78.837 Å
Unit-cell length c length_c	76.605 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	49.056 Å
R factor r_factor	0.1961
R_work r_work	0.1929
R_free r_free	0.2564

Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN

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

Glucokinase 1, putative

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

5brd__assembly_1__model_1

5brd__assembly_1__model_1 | I(q)

5brd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Trypanosoma cruzi glucokinase in complex with inhibitor BENZ-GlcN

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

Glucokinase 1, putative

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

5brd__assembly_1__model_1

5brd__assembly_1__model_1 | I(q)

5brd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)