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- PDB-3bjm: Crystal structure of human DPP-IV in complex with (1S,3S, 5S)-2-[... -

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Basic information

Entry
Database: PDB / ID: 3bjm
TitleCrystal structure of human DPP-IV in complex with (1S,3S, 5S)-2-[(2S)-2-AMINO-2-(3-HYDROXYTRICYCLO[3.3.1.13,7]DEC-1- YL)ACETYL]-2-AZABICYCLO[3.1.0]HEXANE-3-CARBONITRILE (CAS), (1S,3S,5S)-2-((2S)-2-AMINO-2-(3-HYDROXYADAMANTAN-1- YL)ACETYL)-2-AZABICYCLO[3.1.0]HEXANE-3-CARBONITRILE (IUPAC), OR BMS-477118
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE / EXOPEPTIDASE / ALPHA/BETA HYDROLASE FOLD / BETA BARREL / BETA PROPELLER / DPP4 / DIMER / PROTEIN:INHIBITOR COMPLEX / Aminopeptidase / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / virus receptor activity / lamellipodium / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Alpha/Beta hydrolase fold, catalytic domain ...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-BJM / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.35 Å
AuthorsKlei, H.E.
CitationJournal: Protein Sci. / Year: 2008
Title: Involvement of DPP-IV catalytic residues in enzyme-saxagliptin complex formation.
Authors: Metzler, W.J. / Yanchunas, J. / Weigelt, C. / Kish, K. / Klei, H.E. / Xie, D. / Zhang, Y. / Corbett, M. / Tamura, J.K. / He, B. / Hamann, L.G. / Kirby, M.S. / Marcinkeviciene, J.
History
DepositionDec 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 27, 2011Group: Other
Revision 1.3Oct 29, 2014Group: Database references
Revision 1.4Apr 20, 2016Group: Non-polymer description
Revision 1.5Oct 25, 2017Group: Advisory / Data collection / Refinement description
Category: diffrn_radiation_wavelength / diffrn_source ...diffrn_radiation_wavelength / diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Feb 14, 2018Group: Non-polymer description / Structure summary / Category: entity
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description
Revision 2.1Jul 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.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_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
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 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,33012
Polymers168,9252
Non-polymers2,40510
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.278, 67.954, 423.816
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 4 / Dipeptidyl peptidase-4 / Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103 / Adenosine deaminase ...Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103 / Adenosine deaminase complexing protein 2 / ADABP


Mass: 84462.617 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / 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
#3: Chemical ChemComp-BJM / (2~{S})-2-azanyl-1-[(1~{S},3~{S},5~{S})-3-(iminomethyl)-2-azabicyclo[3.1.0]hexan-2-yl]-2-[(5~{R},7~{S})-3-oxidanyl-1-ad amantyl]ethanone / Saxagliptin, bound form / Saxagliptin


Mass: 317.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H27N3O2 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.78 Å3/Da / Density % sol: 55.79 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 78823

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
CNX2005refinement
RefinementMethod to determine structure: molecular replacement / Resolution: 2.35→45.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2474529.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1576 2 %RANDOM
Rwork0.213 ---
obs0.214 78763 98.2 %-
all-78763 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.969 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1--8.7 Å20 Å20 Å2
2--14.88 Å20 Å2
3----6.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.35→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11926 0 158 154 12238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it3.262
X-RAY DIFFRACTIONc_scangle_it4.272.5
LS refinement shellResolution: 2.35→2.4 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.352 96 2.1 %
Rwork0.316 4394 -
all-4490 -
obs--42.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramwater.top
X-RAY DIFFRACTION3water_rep.paramion.top
X-RAY DIFFRACTION4ion.paramcarbohydrate.top
X-RAY DIFFRACTION5carbohydrate.param

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