9xyl

Human prolyl endopeptidase (PREP) - complex with S17092

Method: X-RAY DIFFRACTION

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

Prolyl endopeptidase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GLYCEROL × 4 THIOCYANATE ION × 1 DI(HYDROXYETHYL)ETHER × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GLYCEROL × 3 THIOCYANATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GLYCEROL × 2 THIOCYANATE ION × 2 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GLYCEROL × 1 THIOCYANATE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GLYCEROL × 2 THIOCYANATE ION × 2 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPCE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–711； UniProt 1–710 Author chain B； PDBConstruct 2–711； UniProt 1–710 Author chain C； PDBConstruct 2–711； UniProt 1–710 Author chain D； PDBConstruct 2–711； UniProt 1–710 Author chain E； PDBConstruct 2–711； UniProt 1–710 Author chain F； PDBConstruct 2–711； 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	9xyl
Deposition date deposition_date	2025-08-26
Structure title title	Human prolyl endopeptidase (PREP) - complex with S17092
Keywords keywords	inhibitor-bound, peptide cleavage, 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.

9xyl__assembly_1__model_1

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

Download this curve (.dat)

9xyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9xyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.88 Å
Rg (electron density)	25.74 Å
Total Rg	26.71 Å
Atom count	11318
Residues	707
Excluded volume	101870 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9xyl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9xyl__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9xyl__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9xyl__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`9xyl__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`9xyl__assembly_6__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 (7)

Entity 1 Entity 1 polymer

Description description	Prolyl endopeptidase
Molecular weight formula_weight	80851.4 kDa
EC 编号 ec_number	3.4.21.26
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	69507

GMLSLQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRQSPNYRVINIDFRDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNILQLHDLTTGALLKTFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQSNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	{(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone
Molecular weight formula_weight	384.5 kDa
Source method src_method	syn
Copy count entity_count	6

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	12

Entity 4 Entity 4 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1747

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Unit-cell length a length_a	67.187 Å
Unit-cell length b length_b	105.735 Å
Unit-cell length c length_c	155.670 Å
Unit-cell angle α angle_alpha	81.78 °
Unit-cell angle β angle_beta	89.79 °
Unit-cell angle γ angle_gamma	89.70 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	29.680 Å
R factor r_factor	—
R_work r_work	0.1907
R_free r_free	0.2489

Human prolyl endopeptidase (PREP) - complex with S17092

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

9xyl__assembly_1__model_1

9xyl__assembly_1__model_1 | I(q)

9xyl__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Human prolyl endopeptidase (PREP) - complex with S17092

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

9xyl__assembly_1__model_1

9xyl__assembly_1__model_1 | I(q)

9xyl__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)