SAXSdb — 2ebj

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

Pyrrolidone carboxyl peptidase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SJW4_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–192； UniProt 1–192 Author chain B； PDBConstruct 1–192； UniProt 1–192

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	2ebj
Deposition date deposition_date	2007-02-08
Structure title title	Crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus
Keywords keywords	;pyrrolidone carboxyl peptidase, Thermus thermophilus, TTHA0888, degradation of proteins and peptides, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, HYDROLASE ;; HYDROLASE
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.

2ebj__assembly_1__model_1

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

Download this curve (.dat)

2ebj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ebj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.03 Å
Rg (electron density)	28.00 Å
Total Rg	28.87 Å
Atom count	5914
Residues	768
Excluded volume	106570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ebj__assembly_1__model_1`	tetrameric （4）	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 (2)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ebja_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
Family Family family	c.56.4.0 — automated matches

Domain ID domain_id	d2ebjb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.4 — Pyrrolidone carboxyl peptidase (pyroglutamate aminopeptidase)
Family Family family	c.56.4.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2ebjA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

Domain ID domain_id	2ebjB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	20 — Peptidase C15, pyroglutamyl peptidase I-like

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Unit-cell length a length_a	51.913 Å
Unit-cell length b length_b	118.382 Å
Unit-cell length c length_c	143.581 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	16

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	19.820 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2570

Description description	Pyrrolidone carboxyl peptidase
Molecular weight formula_weight	21145.6 kDa
EC 编号 ec_number	3.4.19.3
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3196

Crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus

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

Pyrrolidone carboxyl peptidase

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

2ebj__assembly_1__model_1

2ebj__assembly_1__model_1 | I(q)

2ebj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	239

Crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus

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

Pyrrolidone carboxyl peptidase

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

2ebj__assembly_1__model_1

2ebj__assembly_1__model_1 | I(q)

2ebj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)