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- PDB-5ehh: Structure of human DPP3 in complex with endomorphin-2. -

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Basic information

Entry
Database: PDB / ID: 5ehh
TitleStructure of human DPP3 in complex with endomorphin-2.
Components
  • Dipeptidyl peptidase 3
  • Endomorphin-2
KeywordsHYDROLASE / Inhibitor-complex / Peptidase / Zinc-hydrolase
Function / homology
Function and homology information


dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / protein catabolic process / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / zinc ion binding / extracellular exosome ...dipeptidyl-peptidase III / metalloexopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / protein catabolic process / KEAP1-NFE2L2 pathway / Neddylation / proteolysis / zinc ion binding / extracellular exosome / 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: 2.38 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 28, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidyl peptidase 3
B: Endomorphin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2726
Polymers82,1192
Non-polymers1534
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-65 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.035, 105.457, 64.719
Angle α, β, γ (deg.)90.00, 93.49, 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 / Fragment: UNP residues 1-726 / 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 BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: Q9NY33, dipeptidyl-peptidase III
#2: Protein/peptide Endomorphin-2


Mass: 570.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Human opioid peptide endomorphin-2 / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 274 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.: 270 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 8.2
Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH-8.2.
PH range: 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 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: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.38→49.09 Å / Num. all: 32020 / Num. obs: 32020 / % possible obs: 98.87 % / Redundancy: 3.4 % / Biso Wilson estimate: 40.63 Å2 / Rmerge(I) obs: 0.0914 / Rsym value: 0.0914 / Net I/σ(I): 10.61
Reflection shellResolution: 2.38→2.463 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.78 / % possible all: 95.37

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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: 2.38→49.09 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1601 5 %Random selection
Rwork0.1938 ---
obs0.1959 32016 98.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4 Å2
Refinement stepCycle: LAST / Resolution: 2.38→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5787 0 4 270 6061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035927
X-RAY DIFFRACTIONf_angle_d0.578025
X-RAY DIFFRACTIONf_dihedral_angle_d11.7612182
X-RAY DIFFRACTIONf_chiral_restr0.023863
X-RAY DIFFRACTIONf_plane_restr0.0031053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4550.35971390.29292655X-RAY DIFFRACTION95
2.455-2.54280.32871450.27312749X-RAY DIFFRACTION99
2.5428-2.64460.3051460.26182777X-RAY DIFFRACTION99
2.6446-2.76490.29321460.24622778X-RAY DIFFRACTION100
2.7649-2.91070.27651450.23572750X-RAY DIFFRACTION100
2.9107-3.0930.28981480.2352801X-RAY DIFFRACTION100
3.093-3.33180.3091450.21552762X-RAY DIFFRACTION99
3.3318-3.66690.28071450.19562752X-RAY DIFFRACTION99
3.6669-4.19730.19731460.16482775X-RAY DIFFRACTION99
4.1973-5.28720.15961470.14482789X-RAY DIFFRACTION99
5.2872-49.10.17631490.15772827X-RAY DIFFRACTION99

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