SAXSdb — 1pv9

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

Xaa-Pro dipeptidase

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEPQ_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–348； UniProt 1–348 Author chain B； PDBConstruct 1–348； UniProt 1–348

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	1pv9
Deposition date deposition_date	2003-06-27
Structure title title	Prolidase from Pyrococcus furiosus
Keywords keywords	prolidase, peptidase, 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.

1pv9__assembly_1__model_1

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

Download this curve (.dat)

1pv9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pv9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.69 Å
Rg (electron density)	25.52 Å
Total Rg	26.45 Å
Atom count	5200
Residues	655
Excluded volume	93609 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pv9__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	Xaa-Pro dipeptidase
Molecular weight formula_weight	39443.2 kDa
EC 编号 ec_number	3.4.13.9
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	5376

MKERLEKLVKFMDENSIDRVFIAKPVNVYYFSGTSPLGGGYIIVDGDEATLYVPELEYEMAKEESKLPVVKFKKFDEIYEILKNTETLGIEGTLSYSMVENFKEKSNVKEFKKIDDVIKDLRIIKTKEEIEIIEKACEIADKAVMAAIEEITEGKREREVAAKVEYLMKMNGAEKPAFDTIIASGHRSALPHGVASDKRIERGDLVVIDLGALYNHYNSDITRTIVVGSPNEKQREIYEIVLEAQKRAVEAAKPGMTAKELDSIAREIIKEYGYGDYFIHSLGHGVGLEIHEWPRISQYDETVLKEGMVITIEPGIYIPKLGGVRIEDTVLITENGAKRLTKTERELL

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1pv9a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1pv9a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

Domain ID domain_id	d1pv9b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1pv9b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (4 domains)

Domain ID domain_id	1pv9A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1pv9A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	1pv9B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1pv9B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

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Unit-cell length a length_a	56.476 Å
Unit-cell length b length_b	97.227 Å
Unit-cell length c length_c	69.882 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.09 °
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	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2464
R_work r_work	0.2447
R_free r_free	0.2773

Prolidase from Pyrococcus furiosus

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

Xaa-Pro dipeptidase

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

1pv9__assembly_1__model_1

1pv9__assembly_1__model_1 | I(q)

1pv9__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Prolidase from Pyrococcus furiosus

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

Xaa-Pro dipeptidase

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

1pv9__assembly_1__model_1

1pv9__assembly_1__model_1 | I(q)

1pv9__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)