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- PDB-5e3c: Structure of human DPP3 in complex with hemorphin like opioid pep... -

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Basic information

Entry
Database: PDB / ID: 5e3c
TitleStructure of human DPP3 in complex with hemorphin like opioid peptide IVYPW
Components
  • Dipeptidyl peptidase 3
  • IVYPW
KeywordsHYDROLASE / Opioid-peptide / Zinc-hydrolase / peptidase / Inhibitor complex
Function / homology
Function and homology information


dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / extracellular exosome / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Fructose-1,6-Bisphosphatase; Chain A, domain 1 - #30 / Alpha-Beta Plaits - #2600 / Dipeptidyl-peptidase 3 / Peptidase family M49 / Peptidase family M49 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Dipeptidyl peptidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.765 Å
AuthorsKumar, P. / Reithofer, V. / Reisinger, M. / Pavkov-Keller, T. / Wallner, S. / Macheroux, P. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: Sci Rep / Year: 2016
Title: Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition.
Authors: Kumar, P. / Reithofer, V. / Reisinger, M. / Wallner, S. / Pavkov-Keller, T. / Macheroux, P. / Gruber, K.
History
DepositionOct 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
B: IVYPW
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3796
Polymers82,2252
Non-polymers1534
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-67 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.669, 106.386, 65.121
Angle α, β, γ (deg.)90.00, 93.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Dipeptidyl peptidase 3 / Dipeptidyl aminopeptidase III / Dipeptidyl arylamidase III / Dipeptidyl peptidase III / DPP III / ...Dipeptidyl aminopeptidase III / Dipeptidyl arylamidase III / Dipeptidyl peptidase III / DPP III / Enkephalinase B


Mass: 81548.688 Da / Num. of mol.: 1 / Mutation: C19S, E207C, E451A, S491C, C519S, C654S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP3 / Plasmid: PET28MHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NY33, dipeptidyl-peptidase III
#2: Protein/peptide IVYPW


Mass: 676.802 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: hemorphin like opioid peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 33 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.056 Sodium phosphate monobasic monohydrate, 1.344M Potassium phosphate dibasic
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.76→45.56 Å / Num. all: 20651 / Num. obs: 20651 / % possible obs: 97.92 % / Redundancy: 3.8 % / Biso Wilson estimate: 57.44 Å2 / Rmerge(I) obs: 0.211 / Rsym value: 0.211 / Net I/σ(I): 4.39
Reflection shellResolution: 2.76→2.86 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5016 / Mean I/σ(I) obs: 1.44 / % possible all: 84.87

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T6B

3t6b


Resolution: 2.765→45.56 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1033 5.01 %Random selection
Rwork0.204 ---
obs0.2064 20628 97.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.3 Å2
Refinement stepCycle: LAST / Resolution: 2.765→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 4 29 5827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035942
X-RAY DIFFRACTIONf_angle_d0.5078050
X-RAY DIFFRACTIONf_dihedral_angle_d10.9572191
X-RAY DIFFRACTIONf_chiral_restr0.02867
X-RAY DIFFRACTIONf_plane_restr0.0031055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7646-2.91040.32391330.26592529X-RAY DIFFRACTION89
2.9104-3.09270.28391520.25162880X-RAY DIFFRACTION100
3.0927-3.33140.33491480.24252823X-RAY DIFFRACTION100
3.3314-3.66650.26441490.22232819X-RAY DIFFRACTION98
3.6665-4.19670.25391480.20672793X-RAY DIFFRACTION98
4.1967-5.28620.20991500.17552857X-RAY DIFFRACTION100
5.2862-45.570.22861530.1772894X-RAY DIFFRACTION99

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