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- PDB-5vta: Co-Crystal Structure of DPPIV with a Chemibody Inhibitor -

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Basic information

Entry
Database: PDB / ID: 5vta
TitleCo-Crystal Structure of DPPIV with a Chemibody Inhibitor
Components
  • Dipeptidyl peptidase 4
  • Fab heavy chain
  • Fab light chain
KeywordsHYDROLASE / chemibody
Function / homology
Function and homology information


B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / positive regulation of natural killer cell mediated immunity / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / psychomotor behavior / dipeptidyl-peptidase IV ...B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / positive regulation of natural killer cell mediated immunity / negative regulation of neutrophil chemotaxis / 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 / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / collagen binding / T cell costimulation / T cell activation / serine-type peptidase activity / peptide binding / protein catabolic process / lamellipodium / virus receptor activity / protease binding / cell adhesion / response to hypoxia / 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 / identical protein binding / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-9K4 / DI(HYDROXYETHYL)ETHER / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWang, Z. / Johnstone, S. / Cheng, A.
CitationJournal: Sci Rep / Year: 2018
Title: Structure-guided Discovery of Dual-recognition Chemibodies.
Authors: Cheng, A.C. / Doherty, E.M. / Johnstone, S. / DiMauro, E.F. / Dao, J. / Luthra, A. / Ye, J. / Tang, J. / Nixey, T. / Min, X. / Tagari, P. / Miranda, L.P. / Wang, Z.
History
DepositionMay 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
L: Fab light chain
E: Fab light chain
H: Fab heavy chain
F: Fab heavy chain
G: Fab light chain
I: Fab heavy chain
J: Fab light chain
K: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)535,92351
Polymers527,31412
Non-polymers8,61039
Water2,126118
1
A: Dipeptidyl peptidase 4
J: Fab light chain
K: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,29716
Polymers131,8283
Non-polymers2,46913
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptidyl peptidase 4
G: Fab light chain
I: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4839
Polymers131,8283
Non-polymers1,6556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dipeptidyl peptidase 4
E: Fab light chain
F: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,17415
Polymers131,8283
Non-polymers2,34512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dipeptidyl peptidase 4
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,97011
Polymers131,8283
Non-polymers2,1418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.325, 123.229, 129.018
Angle α, β, γ (deg.)62.340, 77.210, 75.910
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 8 molecules LEGJHFIK

#2: Antibody
Fab light chain


Mass: 23031.551 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Antibody
Fab heavy chain


Mass: 23267.041 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 25 molecules ABCD

#1: Protein
Dipeptidyl peptidase 4 / Bile canaliculus domain-specific membrane glycoprotein / Dipeptidyl peptidase IV / DPP IV / GP110 ...Bile canaliculus domain-specific membrane glycoprotein / Dipeptidyl peptidase IV / DPP IV / GP110 glycoprotein / T-cell activation antigen CD26


Mass: 85529.836 Da / Num. of mol.: 4 / Fragment: residues 37-767
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dpp4, Cd26 / Production host: Homo sapiens (human) / References: UniProt: P14740, dipeptidyl-peptidase IV
#4: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 21
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 , 5 types, 136 molecules

#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-9K4 / 2-{4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]piperazin-1-yl}-N-(22-oxo-3,6,9,12,15,18-hexaoxa-21-azatricosan-1-yl)acetamide


Mass: 707.779 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C32H52F3N5O9
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 1000, sodium citrate tribasic dihydrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→29.96 Å / Num. obs: 138383 / % possible obs: 89 % / Redundancy: 2.7 % / CC1/2: 0.977 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.094 / Rrim(I) all: 0.164 / Net I/σ(I): 5.4 / Num. measured all: 371086 / Scaling rejects: 70
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.852.20.7941203855900.5220.6031.003172.7
15.34-29.963.20.08625878030.9830.0580.10512.385.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
SCALA0.5.27data scaling
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.824 / SU B: 23.751 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 6869 5 %RANDOM
Rwork0.2497 ---
obs0.2522 130806 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.16 Å2 / Biso mean: 50.615 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å2-0.58 Å2-1.09 Å2
2---0.62 Å20.43 Å2
3----3.11 Å2
Refinement stepCycle: final / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33201 0 549 118 33868
Biso mean--68.73 19.97 -
Num. residues----4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01934712
X-RAY DIFFRACTIONr_bond_other_d0.0020.0231496
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.94747153
X-RAY DIFFRACTIONr_angle_other_deg1.007372714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42854143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84824.2071569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.106155536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.215135
X-RAY DIFFRACTIONr_chiral_restr0.0940.25091
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02138950
X-RAY DIFFRACTIONr_gen_planes_other0.0020.028235
LS refinement shellResolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 422 -
Rwork0.377 7861 -
all-8283 -
obs--72.66 %

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