2o2d

Crystal structure of phosphoglucose isomerase from Trypanosoma brucei complexed with citrate

Method: X-RAY DIFFRACTION

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

Glucose-6-phosphate isomerase, glycosomal

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 2	CITRIC ACID × 2 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CITRIC ACID × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G6PI_TRYBB
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–607； UniProt 1–607 Author chain B； PDBConstruct 1–607； UniProt 1–607 Author chain C； PDBConstruct 1–607； UniProt 1–607

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	2o2d
Deposition date deposition_date	2006-11-29
Structure title title	Crystal structure of phosphoglucose isomerase from Trypanosoma brucei complexed with citrate
Keywords keywords	dimer, ISOMERASE; ISOMERASE
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.

2o2d__assembly_1__model_1

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

Download this curve (.dat)

2o2d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o2d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.95 Å
Rg (electron density)	28.46 Å
Total Rg	29.41 Å
Atom count	8992
Residues	1136
Excluded volume	159930 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o2d__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2o2d__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Glucose-6-phosphate isomerase, glycosomal
Molecular weight formula_weight	68458.7 kDa
EC 编号 ec_number	5.3.1.9
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	14574

MSSYLDDLRIDLAASPASGGSASIAVGSFNIPYEVTRRLKGVGADADTTLTSCASWTQLQKLYEQYGDEPIKKHFETDSERGQRYSVKVSLGSKDENFLFLDYSKSHINDEIKCALLRLAEERGIRQFVQSVFRGERVNTTENRPVLHIALRNRSNRPIYVDGKDVMPAVNKVLDQMRSFSEKVRTGEWKGHTGKAIRHVVNIGIGGSDLGPVMATEALKPFSQRDLSLHFVSNVDGTHIAEVLKSIDIEATLFIVASKTFTTQETITNALSARRALLDYLRSRGIDEKGSVAKHFVALSTNNQKVKEFGIDEENMFQFWDWVGGRYSMWSAIGLPIMISIGYENFVELLTGAHVIDEHFANAPPEQNVPLLLALVGVWYINFFGAVTHAILPYDQYLWRLPAYLQQLDMESNGKYVTRSGKTVSTLTGPIIFGEAGTNGQHAFYQLIHQGTNLIPCDFIGAIQSQNKIGDHHKIFMSNFFAQTEALMIGKSPSEVRRELEAAGERSAEKINALLPHKTFIGGRPSNTLLIKSLTPRALGAIIAMYEHKVLVQGAIWGIDSYDQWGVELGKVLAKSILPQLRPGMRVNNHDSSTNGLINMFNELSHLHHHHHH

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	3

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1120

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2o2da_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.80 — SIS domain
Superfamily Superfamily superfamily	c.80.1 — SIS domain
Family Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

Domain ID domain_id	d2o2db_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.80 — SIS domain
Superfamily Superfamily superfamily	c.80.1 — SIS domain
Family Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

Domain ID domain_id	d2o2dc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.80 — SIS domain
Superfamily Superfamily superfamily	c.80.1 — SIS domain
Family Family family	c.80.1.2 — Phosphoglucose isomerase, PGI

CATH v4.4 (9 domains)

Domain ID domain_id	2o2dA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	2o2dA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	2o2dA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2o2dB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	2o2dB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	2o2dB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2o2dC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	2o2dC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	2o2dC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1390 — Phosphoglucose isomerase, C-terminal domain
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	124.203 Å
Unit-cell length b length_b	217.391 Å
Unit-cell length c length_c	126.433 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	24

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	—
R_work r_work	0.2133
R_free r_free	0.2356

Crystal structure of phosphoglucose isomerase from Trypanosoma brucei complexed with citrate

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

Glucose-6-phosphate isomerase, glycosomal

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

2o2d__assembly_1__model_1

2o2d__assembly_1__model_1 | I(q)

2o2d__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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of phosphoglucose isomerase from Trypanosoma brucei complexed with citrate

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

Glucose-6-phosphate isomerase, glycosomal

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

2o2d__assembly_1__model_1

2o2d__assembly_1__model_1 | I(q)

2o2d__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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)