SAXSdb — 6hje

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

Proline racemase A

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	PHOSPHATE ION × 1 2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRCMA_TRYCC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–393； UniProt 32–423 Author chain B； PDBConstruct 2–393； UniProt 32–423

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	6hje
Deposition date deposition_date	2018-09-03
Structure title title	Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27
Keywords keywords	Proline Racemase, Drug Design, Michael Reaction, 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.

6hje__assembly_1__model_1

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

Download this curve (.dat)

6hje__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hje__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.14 Å
Rg (electron density)	27.51 Å
Total Rg	28.24 Å
Atom count	5448
Residues	713
Excluded volume	97216 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hje__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 (4)

Entity 1 Entity 1 polymer

Description description	Proline racemase A
Molecular weight formula_weight	45796.2 kDa
EC 编号 ec_number	5.1.1.4
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	5872

MGQEKLLFDQKYKIIKGEKKEKKKNQRANRREHQQKREIMRFKKSFTCIDMHTEGEAARIVTSGLPHIPGSNMAEKKAYLQENMDYLRRGIMLEPRGHDDMFGAFLFDPIEEGADLGIVFMDTGGYLNMCGHNSIAAVTAAVETGIVSVPAKATNVPVVLDTPAGLVRGTAHLQSGTESEVSNASIINVPSFLYQQDVVVVLPKPYGEVRVDIAFGGNFFAIVPAEQLGIDISVQNLSRLQEAGELLRTEINRSVKVQHPQLPHINTVDCVEIYGPPTNPEANYKNVVIFGNRQADRSPCGTGTSAKMATLYAKGQLRIGETFVYESILGSLFQGRVLGEERIPGVKVPVTKDAEEGMLVVTAEITGKAFIMGFNTMLFDPTDPFKNGFTLKQYIWSSSVDKLAAALEHHHHHH

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	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid
Molecular weight formula_weight	142.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	389

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6hjea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.0 — automated matches

Domain ID domain_id	d6hjea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6hjeb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.21 — Diaminopimelate epimerase-like
Superfamily Superfamily superfamily	d.21.1 — Diaminopimelate epimerase-like
Family Family family	d.21.1.0 — automated matches

Domain ID domain_id	d6hjeb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	6hjeA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	6hjeA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	6hjeB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

Domain ID domain_id	6hjeB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Diaminopimelate Epimerase; Chain A, domain 1

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Unit-cell length a length_a	133.233 Å
Unit-cell length b length_b	90.640 Å
Unit-cell length c length_c	85.394 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	126.04 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.1780
R_work r_work	0.1770
R_free r_free	0.2300

Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27

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

Proline racemase A

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

6hje__assembly_1__model_1

6hje__assembly_1__model_1 | I(q)

6hje__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27

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

Proline racemase A

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

6hje__assembly_1__model_1

6hje__assembly_1__model_1 | I(q)

6hje__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)