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- PDB-1pfq: crystal structure of human apo dipeptidyl peptidase IV / CD26 -

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Basic information

Entry
Database: PDB / ID: 1pfq
Titlecrystal structure of human apo dipeptidyl peptidase IV / CD26
ComponentsDipeptidyl peptidase IV soluble form
KeywordsHYDROLASE / MCH_1
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / membrane fusion / receptor-mediated endocytosis of virus by host cell / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
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 ...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
Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsOefner, C. / D'Arcy, A. / Mac Sweeney, A. / Pierau, S. / Gardiner, R. / Dale, G.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine.
Authors: Oefner, C. / D'Arcy, A. / Mac Sweeney, A. / Pierau, S. / Gardiner, R. / Dale, G.E.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidyl peptidase IV soluble form
B: Dipeptidyl peptidase IV soluble form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,3856
Polymers169,5002
Non-polymers8854
Water8,503472
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-2 kcal/mol
Surface area60340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.031, 118.142, 184.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dipeptidyl peptidase IV soluble form / DPP IV / T-cell activation antigen CD26 / TP103 / Adenosine deaminase complexing protein-2 / ADABP


Mass: 84749.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4 OR ADCP2 OR CD26 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %PEG33501reservoir
2200 mM1reservoirMgCl2
3100 mMHEPES1reservoirpH7.5
425 mMTris1droppH7.5
5100 mM1dropNaCl
62 mMTCEP1drop
75 %glycerol1drop
820 mg/mlprotein1drop

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 122631 / % possible obs: 99.7 % / Rsym value: 0.126
Reflection
*PLUS
Num. measured all: 803624 / Rmerge(I) obs: 0.126
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1

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Processing

SoftwareName: REFMAC / Version: 5 / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 8.242 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Reflection file contains Friedel's pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.29807 6101 5 %RANDOM
Rwork0.25396 ---
all0.25614 ---
obs0.25614 115106 98.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---1.04 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11890 0 56 472 12418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02112307
X-RAY DIFFRACTIONr_bond_other_d00.0210515
X-RAY DIFFRACTIONr_angle_refined_deg0.6491.93116745
X-RAY DIFFRACTIONr_angle_other_deg0.527324479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08531450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.363152064
X-RAY DIFFRACTIONr_chiral_restr0.0430.21771
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0213690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022658
X-RAY DIFFRACTIONr_nbd_refined0.2560.32806
X-RAY DIFFRACTIONr_nbd_other0.2550.311100
X-RAY DIFFRACTIONr_nbtor_other0.7470.54
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.5748
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1840.517
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5010.355
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4890.3102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4830.515
X-RAY DIFFRACTIONr_mcbond_it0.61627239
X-RAY DIFFRACTIONr_mcangle_it1.141311741
X-RAY DIFFRACTIONr_scbond_it0.62125068
X-RAY DIFFRACTIONr_scangle_it0.88935004
LS refinement shellResolution: 1.9→2.002 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.338 829
Rwork0.311 15551
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.298 / Rfactor Rwork: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.004
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg0.65

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