SAXSdb — 5e3c

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

Dipeptidyl peptidase 3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–726	Mutation：C19S, E207C, E451A, S491C, C519S, C654S	IVYPW × 1 ZN ZINC ION × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.056 Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic	Resolution 2.77 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5E3C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3FVY Crystal structure of human Dipeptidyl Peptidase III Deposited 2009-01-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–726（726 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；20% PEG3350. 0.2M MgForm, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 1.90 Å R-free 0.219
3T6B Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms Deposited 2011-07-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–726（726 aa）	Mutation：E451A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；293 K；0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2, vapor diffusion, temperature 293K	Resolution 2.40 Å R-free 0.258
3T6B Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms Deposited 2011-07-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–726（726 aa）	Mutation：E451A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；293 K；0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2, vapor diffusion, temperature 293K	Resolution 2.40 Å R-free 0.258
3T6J Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 3.0 Angstroms Deposited 2011-07-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–726（726 aa）	Mutation：E451A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；293 K；0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH 8.2, vapor diffusion, temperature 293K	Resolution 2.98 Å R-free 0.268
5E2Q Structure of human DPP3 in complex with angiotensin-II Deposited 2015-10-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–726（726 aa）	Mutation：C19S, E207C, E451A, S491C, C519S, C654S	MG MAGNESIUM ION × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.056 M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate dibasic monohydrate	Resolution 2.40 Å R-free 0.247
5E33 Structure of human DPP3 in complex with met-enkephalin Deposited 2015-10-01	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–726（726 aa）	Mutation：C19S, E207C, E451A, S491C, C519S, C654S	ZN ZINC ION × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.056M Sodium phosphate monobasic monohydrate, 1.344M Potassium phospahte dibasic, pH- 8.2	Resolution 1.84 Å R-free 0.224
5E3A Structure of human DPP3 in complex with opioid peptide leu-enkephalin Deposited 2015-10-02	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–726（726 aa）	Mutation：C19S, E207C, E451A, S491C, C519S, C654S	ZN ZINC ION × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.056M SODIUM PHOSPHATE MONOBASIC MONOHYDRATE, 1.344M POTASSIUM PHOSPHATE DIBASIC	Resolution 2.05 Å R-free 0.260
5EGY Structure of ligand free human DPP3 in closed form. Deposited 2015-10-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–726（726 aa）	Mutation：C19S, E207C, E451A, S491C, C519S, C654S	ZN ZINC ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.056 M Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic, pH- 8.2, 293K	Resolution 2.74 Å R-free 0.254
5EHH Structure of human DPP3 in complex with endomorphin-2. Deposited 2015-10-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–726（726 aa） Fragment：UNP residues 1-726	Mutation：C19S, E207C, E451A, S491C, C519S, C654S	ZN ZINC ION × 1 MG MAGNESIUM ION × 2 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.2；293.15 K；0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH-8.2.	Resolution 2.38 Å R-free 0.237
7OUP Structure of human DPP3 in complex with a hydroxyethylene transition state peptidomimetic Deposited 2021-06-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–737（737 aa）	Mutation：E451A	ZN ZINC ION × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；0.056 M sodium phosphate monobasic monohydrate, 1.344 M potassium phosphate dibasic monohydrate	Resolution 2.65 Å R-free 0.253

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPP3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–726； UniProt 1–726

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	5e3c
Deposition date deposition_date	2015-10-02
Structure title title	Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW
Keywords keywords	Opioid-peptide, Zinc-hydrolase, peptidase, Inhibitor complex, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.71 Å
Radius of gyration Rg (electron density) rg_electron	25.40 Å
Forward intensity I(0) i0	106392000.00
Molecular weight molecular_weight	82066.0 kDa
Excluded volume excluded_volume	103020 Å³
Envelope volume envelope_volume	121630 Å³
Hydration-shell volume shell_volume	38033 Å³
Envelope diameter envelope_diameter	85.5 Å
Shell Rg shell_rg	34.26 Å
Envelope Rg envelope_rg	25.52 Å
Shape Rg shape_rg	25.38 Å
Total Rg total_rg	26.35 Å
Total atoms total_atoms	5798
Residues n_residues	729
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.0 Å
Rg (real space) rg_real	26.52 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	1.0640e+08
I(0) uncertainty (real space) i0_real_error	1.4060e+06
Rg (reciprocal space) rg_reciprocal	26.58 Å
I(0) (reciprocal space) i0_reciprocal	106400000.0000
Solution quality estimate total_estimate	0.6908
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.8 Å
Skewness Skewness skewness	0.122
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	43860000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 0.089; Positv: 1.000; Valcen: 0.985; Smooth: 0.984

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Dipeptidyl peptidase 3
Molecular weight formula_weight	81548.7 kDa
EC 编号 ec_number	3.4.14.4
Mutation mutation	C19S, E207C, E451A, S491C, C519S, C654S
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	5835

MADTQYILPNDIGVSSLDSREAFRLLSPTERLYAYHLSRAAWYGGLAVLLQTSPEAPYIYALLSRLFRAQDPDQLRQHALAEGLTEEEYQAFLVYAAGVYSNMGNYKSFGDTKFVPNLPKEKLERVILGSEAAQQHPEEVRGLWQTCGELMFSLEPRLRHLGLGKEGITTYFSGNCTMEDAKLAQDFLDSQNLSAYNTRLFKEVDGCGKPYYEVRLASVLGSEPSLDSEVTSKLKSYEFRGSPFQVTRGDYAPILQKVVEQLEKAKAYAANSHQGQMLAQYIESFTQGSIEAHKRGSRFWIQDKGPIVESYIGFIESYRDPFGSRGEFEGFVAVVNKAMSAKFERLVASAEQLLKELPWPPTFEKDKFLTPDFTSLDVLTFAGSGIPAGINIPNYDDLRQTEGFKNVSLGNVLAVAYATQREKLTFLEEDDKDLYILWKGPSFDVQVGLHALLGHGSGKLFVQDEKGAFNFDQETVINPETGEQIQSWYRCGETWDSKFSTIASSYEECRAESVGLYLSLHPQVLEIFGFEGADAEDVIYVNWLNMVRAGLLALEFYTPEAFNWRQAHMQARFVILRVLLEAGEGLVTITPTTGSDGRPDARVRLDRSKIRSVGKPALERFLRRLQVLKSTGDVAGGRALYEGYATVTDAPPESFLTLRDTVLLRKESRKLIVQPNTRLEGSDVQLLEYEASAAGLIRSFSERFPEDGPELEEILTQLATADARFW

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	IVYPW
Molecular weight formula_weight	676.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

IVYPW

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5e3cA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	5e3cA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2600 —

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8. Citations (1)

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Unit-cell length a length_a	120.669 Å
Unit-cell length b length_b	106.386 Å
Unit-cell length c length_c	65.121 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.44 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.765 Å
Low-resolution limit resolution_low	45.560 Å
R factor r_factor	0.2064
R_work r_work	0.2040
R_free r_free	0.2528

fit	/app/data/saxs_computation/e3/5e3c/5e3c.fit
pddf	/app/data/pr_computation/e3/5e3c/5e3c.pr.out
profile	/app/data/saxs_computation/e3/5e3c/5e3c.dat

Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW

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

Dipeptidyl peptidase 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)