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3t6b

Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms

Method: X-RAY DIFFRACTION Dmax: 131.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dipeptidyl peptidase 3

Homo sapiens

UniProt Q9NY33

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：E451A Tynorphin × 1 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–726 Mutation：E451A Tynorphin × 1 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

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 3T6B 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
3T6J Structure of human DPPIII in complex with the opioid peptide Tynorphin, at 3.0 Angstroms Deposited 2011-07-28 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 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：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 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：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 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：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
5E3C Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW Deposited 2015-10-02 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：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；0.056 Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic
Resolution 2.77 Å R-free 0.253
5EGY Structure of ligand free human DPP3 in closed form. Deposited 2015-10-27 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）
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 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） 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 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 9 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 Author chain B； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 3t6b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3t6b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3t6b
Deposition date deposition_date2011-07-28
Structure title titleStructure of human DPPIII in complex with the opioid peptide Tynorphin, at 2.4 Angstroms
Keywords keywordshuman dipeptidylpeptidase III, entropy binding, opioid peptide complex, domain motion, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.94 Å
Radius of gyration Rg (electron density) rg_electron38.58 Å
Forward intensity I(0) i0392648000.00
Molecular weight molecular_weight163910.0 kDa
Excluded volume excluded_volume205770 ų
Envelope volume envelope_volume256580 ų
Hydration-shell volume shell_volume55252 ų
Envelope diameter envelope_diameter141.2 Å
Shell Rg shell_rg44.61 Å
Envelope Rg envelope_rg38.20 Å
Shape Rg shape_rg38.59 Å
Total Rg total_rg38.88 Å
Total atoms total_atoms11592
Residues n_residues1458
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax131.1 Å
Rg (real space) rg_real39.10 Å
Rg uncertainty (real space) rg_real_error1.21 Å
I(0) (real space) i0_real3.9260e+08
I(0) uncertainty (real space) i0_real_error6.8960e+06
Rg (reciprocal space) rg_reciprocal39.01 Å
I(0) (reciprocal space) i0_reciprocal392600000.0000
Solution quality estimate total_estimate0.8620
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.6 Å
Skewness Skewness skewness0.431
Kurtosis Kurtosis kurtosis-0.415
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha91860000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.807
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3t6bA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3t6bA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2600 —
Domain ID domain_id3t6bB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology540 — Fructose-1,6-Bisphosphatase; Chain A, domain 1
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3t6bB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily2600 —
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8. Citations (1)

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9. Files and Curves (10)