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- PDB-5lls: Porcine dipeptidyl peptidase IV in complex with 8-(3-aminopiperid... -

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Basic information

Entry
Database: PDB / ID: 5lls
TitlePorcine dipeptidyl peptidase IV in complex with 8-(3-aminopiperidin-1-yl)-7-[(2-bromophenyl)methyl]-1,3-dimethyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione
ComponentsDipeptidyl peptidase 4
KeywordsHYDROLASE / peptidase / inhibitor / complex
Function / homology
Function and homology information


Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / anchoring junction / lamellipodium membrane / endocytic vesicle / endothelial cell migration / aminopeptidase activity ...Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / anchoring junction / lamellipodium membrane / endocytic vesicle / endothelial cell migration / aminopeptidase activity / T cell costimulation / lamellipodium / protease binding / cell adhesion / membrane raft / apical plasma membrane / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular region / plasma membrane
Similarity search - Function
Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain ...Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-6Z8 / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.41 Å
AuthorsNar, H. / Blaesse, M.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Comparative Analysis of Binding Kinetics and Thermodynamics of Dipeptidyl Peptidase-4 Inhibitors and Their Relationship to Structure.
Authors: Schnapp, G. / Klein, T. / Hoevels, Y. / Bakker, R.A. / Nar, H.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,42940
Polymers353,3284
Non-polymers11,10136
Water18,3931021
1
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,11320
Polymers176,6642
Non-polymers5,44918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9330 Å2
ΔGint15 kcal/mol
Surface area56770 Å2
MethodPISA
2
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,31620
Polymers176,6642
Non-polymers5,65218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint15 kcal/mol
Surface area56970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.900, 117.680, 133.120
Angle α, β, γ (deg.)112.70, 94.60, 91.20
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dipeptidyl peptidase 4 / Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26


Mass: 88331.984 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P22411, dipeptidyl-peptidase IV

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Sugars , 2 types, 24 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1033 molecules

#4: Chemical
ChemComp-6Z8 / 8-[(3~{R})-3-azanylpiperidin-1-yl]-7-[(2-bromophenyl)methyl]-1,3-dimethyl-purine-2,6-dione


Mass: 447.329 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C19H23BrN6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1021 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 26% PEG 2000, 0.1 M Tris pH 8, 0.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.41→35.28 Å / Num. obs: 111933 / % possible obs: 80.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 49.13 Å2 / Net I/σ(I): 9.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
XSCALEdata scaling
CNXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2AJ8

2aj8


Resolution: 2.41→35.28 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.867 / Rfactor Rfree error: 0.03 / SU R Cruickshank DPI: 1.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.916 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5218 4.88 %RANDOM
Rwork0.19 ---
obs0.192 106928 80.3 %-
Displacement parametersBiso mean: 41.61 Å2
Baniso -1Baniso -2Baniso -3
1--14.4353 Å23.7668 Å2-1.8455 Å2
2--12.3541 Å2-0.8944 Å2
3---2.0812 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: 1 / Resolution: 2.41→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23840 0 706 1021 25567
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00825315HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0134538HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8589SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes612HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3637HARMONIC5
X-RAY DIFFRACTIONt_it25315HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion18.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact29238SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 107 5.04 %
Rwork0.225 2014 -
all0.228 2121 -
obs--21.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4085-0.1490.01470.84010.07290.46880.0077-0.00240.1411-0.0569-0.005-0.0329-0.03110.0114-0.0027-0.24350.0601-0.0182-0.02770.02020.0261-1.81627.46765.7138
20.4225-0.07590.05371.07910.04130.3753-0.01870.018-0.0983-0.13490.01070.12260.0564-0.05250.0079-0.16850.0549-0.0086-0.0375-0.0207-0.05661.3634-27.4398-5.9478
30.3238-0.0659-0.03391.04960.05020.726-0.053-0.04460.02950.1660.0074-0.03-0.0527-0.04820.0456-0.20740.0304-0.0183-0.0349-0.0202-0.05519.165212.839874.4074
40.4270.21290.23240.79210.11670.99210.05950.0158-0.11420.0254-0.0176-0.04670.257-0.0132-0.0419-0.15040.01090.0119-0.10130.0158-0.056912.5271-42.032965.006
51.454-0.06290.83911.588-0.08690.40210.0165-0.03350.01320.14320.0090.02130.1205-0.0036-0.0255-0.14390.12280.05280.04430.00950.0438-1.344622.970716.4885
60.4966-0.0015-0.83761.5367-0.22350.78790.0148-0.0059-0.04570.1541-0.01370.0142-0.11240.0003-0.0011-0.16180.0694-0.0758-0.0006-0.01210.07090.1266-29.32170.219
72.6827-0.2838-1.08611.66020.85531.24810.02220.0093-0.043-0.0385-0.02340.12250-0.09790.0012-0.07950.008-0.08560.01220.0809-0.07179.7804-38.377957.3089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ H|* }

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