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- PDB-7xnm: Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex -

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Basic information

Entry
Database: PDB / ID: 7xnm
TitleStructure of porcine dipeptidyl peptidase 4 inhibitory peptide complex
Components
  • Dipeptidyl peptidase 4 soluble form
  • ILE-LEU-ALA-PRO-PRO-GLU-ARG
KeywordsHYDROLASE / A serine protease subfamily / diabetes mellitus type 2
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 neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase 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 neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / virus receptor activity / lamellipodium / protease binding / response to hypoxia / cell adhesion / membrane raft / apical plasma membrane / signaling receptor binding / serine-type endopeptidase activity / 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 / 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
Similarity search - Domain/homology
Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesSus scrofa (pig)
Crassostrea gigas (Pacific oyster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.58 Å
AuthorsLi, W.Y. / Cao, M.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex
Authors: Li, W.Y. / Cao, M.J.
History
DepositionApr 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidyl peptidase 4 soluble form
B: Dipeptidyl peptidase 4 soluble form
C: ILE-LEU-ALA-PRO-PRO-GLU-ARG
D: ILE-LEU-ALA-PRO-PRO-GLU-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,40914
Polymers170,4504
Non-polymers3,95910
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11070 Å2
ΔGint34 kcal/mol
Surface area58340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)257.340, 75.617, 121.679
Angle α, β, γ (deg.)90.000, 110.199, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Dipeptidyl peptidase 4 soluble form / Dipeptidyl peptidase IV soluble form


Mass: 84429.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P22411, dipeptidyl-peptidase IV
#2: Protein/peptide ILE-LEU-ALA-PRO-PRO-GLU-ARG


Mass: 795.946 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Crassostrea gigas (Pacific oyster)
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 6
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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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
Has ligand of interestN

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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: 3.27 Å3/Da / Density % sol: 62.34 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M ammonium chloride

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Data collection

DiffractionMean temperature: 190 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021 / Details: silicon crystal (111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 3.575→29.48 Å / Num. obs: 26023 / % possible obs: 98.98 % / Redundancy: 6.5 % / Biso Wilson estimate: 63.18 Å2 / CC1/2: 0.999 / Net I/σ(I): 2
Reflection shellResolution: 3.57547→3.6 Å / Num. unique obs: 168262 / CC1/2: 0.717

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wcy

1wcy


Resolution: 3.58→29.48 Å / SU ML: 0.4639 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.6163
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2989 1999 7.68 %
Rwork0.2232 24024 -
obs0.2289 26023 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.02 Å2
Refinement stepCycle: LAST / Resolution: 3.58→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11967 0 260 0 12227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003712577
X-RAY DIFFRACTIONf_angle_d0.675817117
X-RAY DIFFRACTIONf_chiral_restr0.05831858
X-RAY DIFFRACTIONf_plane_restr0.00532162
X-RAY DIFFRACTIONf_dihedral_angle_d10.00081757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.58-3.660.34291260.27021524X-RAY DIFFRACTION90.07
3.66-3.760.34731410.27861679X-RAY DIFFRACTION98.11
3.76-3.870.31561440.25991728X-RAY DIFFRACTION99.42
3.87-40.34051420.25391713X-RAY DIFFRACTION99.3
4-4.140.30611400.22791685X-RAY DIFFRACTION99.73
4.14-4.310.28231450.21671729X-RAY DIFFRACTION99.89
4.31-4.50.30331440.20091746X-RAY DIFFRACTION99.95
4.5-4.740.25371430.18651718X-RAY DIFFRACTION99.84
4.74-5.030.29141430.19991722X-RAY DIFFRACTION100
5.03-5.420.28991440.19951734X-RAY DIFFRACTION99.95
5.42-5.960.28281450.22431735X-RAY DIFFRACTION100
5.96-6.810.2921460.23311758X-RAY DIFFRACTION99.95
6.82-8.550.31941460.22211747X-RAY DIFFRACTION99.84
8.55-29.480.28281500.21391806X-RAY DIFFRACTION99.49
Refinement TLS params.Method: refined / Origin x: -35.6352358714 Å / Origin y: 37.805535237 Å / Origin z: -8.16251610597 Å
111213212223313233
T0.440650357845 Å2-0.00415080318807 Å2-0.0525055871886 Å2-0.507450947578 Å20.0289035790452 Å2--0.516702095874 Å2
L1.14373956009 °2-0.0963567546525 °2-0.142959244948 °2-0.270725731332 °2-0.0210431725296 °2--0.890599528764 °2
S0.0219534883266 Å °0.288167066748 Å °-0.0407619400165 Å °-0.0365057684087 Å °-0.0401515125922 Å °0.0103969244668 Å °-0.0354241064583 Å °-0.186632531256 Å °0.0132919343489 Å °
Refinement TLS groupSelection details: all

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