SAXSdb — 4bcd

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

PROLYL ENDOPEPTIDASE

SUS SCROFA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1-[(2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-pyrrolidin-1-ylcarbonyl-pyrrolidin-1-yl]-4-phenyl-butan-1-one × 1 TRIS(HYDROXYETHYL)AMINOMETHANE × 1 GLYCEROL × 9 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPCE_PIG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–710； UniProt 1–710

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	4bcd
Deposition date deposition_date	2012-10-01
Structure title title	PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BOUND P2-substituted N-acyl-prolylpyrrolidine inhibitor
Keywords keywords	ALPHA-BETA-HYDROLASE, AMNESIA, HYDROLASE, PARKINSONS DISEASE, ALZHEIMERS DISEASE, INHIBITOR; 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.

4bcd__assembly_1__model_1

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

Download this curve (.dat)

4bcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4bcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.95 Å
Rg (electron density)	25.81 Å
Total Rg	26.78 Å
Atom count	5801
Residues	710
Excluded volume	103250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4bcd__assembly_1__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	PROLYL ENDOPEPTIDASE
Molecular weight formula_weight	80864.3 kDa
EC 编号 ec_number	3.4.21.26
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6765

MLSFQYPDVYRDETAIQDYHGHKVCDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNAYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRLINIDFTDPEESKWKVLVPEHEKDVLEWVACVRSNFLVLCYLHDVKNTLQLHDLATGALLKIFPLEVGSVVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVATCANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLIKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNIDWIP

Source Source

Source organism organism	SUS SCROFA
Common name common_name	PIG
NCBI taxonomy ID ncbi_taxonomy_id	9823
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	1-[(2S,4S)-4-[4-(4-fluorophenyl)-1,2,3-triazol-1-yl]-2-pyrrolidin-1-ylcarbonyl-pyrrolidin-1-yl]-4-phenyl-butan-1-one
Molecular weight formula_weight	475.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	TRIS(HYDROXYETHYL)AMINOMETHANE
Molecular weight formula_weight	163.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	964

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4bcda1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.7 — Peptidase/esterase 'gauge' domain
Family Family family	b.69.7.1 — Prolyl oligopeptidase, N-terminal domain

Domain ID domain_id	d4bcda2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.4 — Prolyl oligopeptidase, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	4bcdA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	4bcdA02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	120 — Prolyl oligopeptidase, N-terminal domain

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Unit-cell length a length_a	70.760 Å
Unit-cell length b length_b	99.210 Å
Unit-cell length c length_c	110.950 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	55.470 Å
R factor r_factor	0.1594
R_work r_work	0.1583
R_free r_free	0.1858

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BOUND P2-substituted N-acyl-prolylpyrrolidine inhibitor

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

PROLYL ENDOPEPTIDASE

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

4bcd__assembly_1__model_1

4bcd__assembly_1__model_1 | I(q)

4bcd__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A NON-COVALENTLY BOUND P2-substituted N-acyl-prolylpyrrolidine inhibitor

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

PROLYL ENDOPEPTIDASE

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

4bcd__assembly_1__model_1

4bcd__assembly_1__model_1 | I(q)

4bcd__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)