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- PDB-7zxs: Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based ... -

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Basic information

Entry
Database: PDB / ID: 7zxs
TitleCrystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295
Components(Dipeptidyl peptidase ...) x 2
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE / DPP9
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding ...dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding / nucleus / cytosol
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family ...Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / 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-KBO / DI(HYDROXYETHYL)ETHER / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsRoss, B. / Huber, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9.
Authors: Carvalho, L.A.R. / Ross, B. / Fehr, L. / Bolgi, O. / Wohrle, S. / Lum, K.M. / Podlesainski, D. / Vieira, A.C. / Kiefersauer, R. / Felix, R. / Rodrigues, T. / Lucas, S.D. / Gross, O. / Geiss- ...Authors: Carvalho, L.A.R. / Ross, B. / Fehr, L. / Bolgi, O. / Wohrle, S. / Lum, K.M. / Podlesainski, D. / Vieira, A.C. / Kiefersauer, R. / Felix, R. / Rodrigues, T. / Lucas, S.D. / Gross, O. / Geiss-Friedlander, R. / Cravatt, B.F. / Huber, R. / Kaiser, M. / Moreira, R.
History
DepositionMay 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,29952
Polymers389,6014
Non-polymers4,69848
Water29,7791653
1
A: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,89522
Polymers194,8172
Non-polymers2,07820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,40430
Polymers194,7852
Non-polymers2,61928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.350, 106.176, 121.127
Angle α, β, γ (deg.)65.250, 70.430, 75.860
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA22 - 8653 - 846
21BB22 - 8653 - 846
12AA22 - 8653 - 846
22CC22 - 8653 - 846
13AA22 - 8653 - 846
23DD22 - 8653 - 846
14BB21 - 8652 - 846
24CC21 - 8652 - 846
15BB22 - 8643 - 845
25DD22 - 8643 - 845
16CC22 - 8653 - 846
26DD22 - 8653 - 846

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Dipeptidyl peptidase ... , 2 types, 4 molecules ACBD

#1: Protein Dipeptidyl peptidase 9 / DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / ...DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / Dipeptidyl peptidase-like protein 9 / DPLP9


Mass: 97408.328 Da / Num. of mol.: 2 / Fragment: extcolor{red}{>FRAGMENT<}
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV
#2: Protein Dipeptidyl peptidase 9 / DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / ...DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / Dipeptidyl peptidase-like protein 9 / DPLP9


Mass: 97392.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV

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Non-polymers , 4 types, 1701 molecules

#3: Chemical
ChemComp-KBO / 2-ethyl-2-methanoyl-~{N}-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide


Mass: 458.595 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H34N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1653 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystal is grown in a condition containing PEG 2K MME buffered by Tris pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.807→106.9 Å / Num. obs: 220955 / % possible obs: 64.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 5.4
Reflection shellResolution: 1.807→1.955 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11048 / Rsym value: 0.459 / % possible all: 15.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
X-GENdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOR

6eor


Resolution: 1.81→106.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.678 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1707 0.8 %RANDOM
Rwork0.1752 ---
obs0.1754 219248 64.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.39 Å2 / Biso mean: 34.669 Å2 / Biso min: 16.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20.07 Å2-0.02 Å2
2---0.04 Å2-0.06 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.81→106.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27210 0 281 1653 29144
Biso mean--47.4 39.52 -
Num. residues----3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01327958
X-RAY DIFFRACTIONr_bond_other_d0.0020.01725440
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.64937983
X-RAY DIFFRACTIONr_angle_other_deg1.1911.57358559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18853417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95522.1471439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.978154295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.17915147
X-RAY DIFFRACTIONr_chiral_restr0.0610.23454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231833
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026645
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A97910.03
12B97910.03
21A97650.03
22C97650.03
31A96960.03
32D96960.03
41B98450.03
42C98450.03
51B97900.03
52D97900.03
61C98170.02
62D98170.02
LS refinement shellResolution: 1.81→1.854 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 10 -
Rwork0.284 1059 -
obs--4.22 %

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