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- PDB-7svn: DPP9 IN COMPLEX WITH LIGAND ICeD-1 -

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Basic information

Entry
Database: PDB / ID: 7svn
TitleDPP9 IN COMPLEX WITH LIGAND ICeD-1
ComponentsDipeptidyl peptidase 9
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE
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-CW8 / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsLammens, A. / Hollenstein, K. / Klein, D.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: A Phenotypic Screen Identifies Potent DPP9 Inhibitors Capable of Killing HIV-1 Infected Cells.
Authors: Moore, K.P. / Schwaid, A.G. / Tudor, M. / Park, S. / Beshore, D.C. / Converso, A. / Shipe, W.D. / Anand, R. / Lan, P. / Moningka, R. / Rothman, D.M. / Sun, W. / Chi, A. / Cornella-Taracido, ...Authors: Moore, K.P. / Schwaid, A.G. / Tudor, M. / Park, S. / Beshore, D.C. / Converso, A. / Shipe, W.D. / Anand, R. / Lan, P. / Moningka, R. / Rothman, D.M. / Sun, W. / Chi, A. / Cornella-Taracido, I. / Adam, G.C. / Bahnck-Teets, C. / Carroll, S.S. / Fay, J.F. / Goh, S.L. / Lusen, J. / Quan, S. / Rodriguez, S. / Xu, M. / Andrews, C.L. / Song, C. / Filzen, T. / Li, J. / Hollenstein, K. / Klein, D.J. / Lammens, A. / Lim, U.M. / Fang, Z. / McHale, C. / Li, Y. / Lu, M. / Diamond, T.L. / Howell, B.J. / Zuck, P. / Balibar, C.J.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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 1.2Oct 30, 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)397,8668
Polymers396,8534
Non-polymers1,0134
Water9,854547
1
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,9334
Polymers198,4262
Non-polymers5072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-14 kcal/mol
Surface area66370 Å2
MethodPISA
2
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,9334
Polymers198,4262
Non-polymers5072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-16 kcal/mol
Surface area66130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.789, 117.439, 163.455
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA20 - 86320 - 863
21PROPROLEULEUBB20 - 86320 - 863
12PROPROHISHISAA20 - 86420 - 864
22PROPROHISHISCC20 - 86420 - 864
13ASPASPHISHISAA19 - 86419 - 864
23ASPASPHISHISDD19 - 86419 - 864
14PROPROLEULEUBB20 - 86320 - 863
24PROPROLEULEUCC20 - 86320 - 863
15PROPROLEULEUBB20 - 86320 - 863
25PROPROLEULEUDD20 - 86320 - 863
16PROPROHISHISCC20 - 86420 - 864
26PROPROHISHISDD20 - 86420 - 864

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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: 99213.211 Da / Num. of mol.: 4
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: Chemical
ChemComp-CW8 / (2S,4S)-1-[(2S)-2-amino-2-cyclohexylacetyl]-4-fluoropyrrolidine-2-carbonitrile


Mass: 253.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H20FN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 10% PEG 8000 25% glycerol 0.16 M calcium acetate 0.08 M cacodilate pH 6.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.78→157.52 Å / Num. obs: 103766 / % possible obs: 94.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 1.92
Reflection shellResolution: 2.78→3.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.593 / Num. unique obs: 23973 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOQ

6eoq


Resolution: 2.78→157.52 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.824 / SU B: 23.704 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3489 732 0.7 %RANDOM
Rwork0.267 ---
obs0.2675 103032 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 229.61 Å2 / Biso mean: 42.485 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å2-0 Å2-0.07 Å2
2--2.58 Å20 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.78→157.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26773 0 72 547 27392
Biso mean--44.65 21.1 -
Num. residues----3303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01927079
X-RAY DIFFRACTIONr_bond_other_d0.0040.0224788
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.94236843
X-RAY DIFFRACTIONr_angle_other_deg1.223356862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3553291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04823.321259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1715.0674207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.67115147
X-RAY DIFFRACTIONr_chiral_restr0.090.23900
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02130758
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026621
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A18542
12B18542
21A18442
22C18442
31A18730
32D18730
41B18706
42C18706
51B18632
52D18632
61C18778
62D18778
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 58 -
Rwork0.403 7747 -
all-7805 -
obs--96.74 %

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