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- PDB-7svm: DPP8 IN COMPLEX WITH LIGAND ICeD-2 -

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Basic information

Entry
Database: PDB / ID: 7svm
TitleDPP8 IN COMPLEX WITH LIGAND ICeD-2
ComponentsDipeptidyl peptidase 8
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / aminopeptidase activity / serine-type peptidase activity / immune response / apoptotic process / proteolysis / cytosol / cytoplasm
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / 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
Similarity search - Domain/homology
Chem-D06 / trimethylamine oxide / Dipeptidyl peptidase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 8
B: Dipeptidyl peptidase 8
C: Dipeptidyl peptidase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,75930
Polymers310,4503
Non-polymers5,30927
Water8,521473
1
A: Dipeptidyl peptidase 8
hetero molecules

A: Dipeptidyl peptidase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,30226
Polymers206,9672
Non-polymers5,33624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4750 Å2
ΔGint-16 kcal/mol
Surface area68610 Å2
MethodPISA
2
B: Dipeptidyl peptidase 8
C: Dipeptidyl peptidase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,60717
Polymers206,9672
Non-polymers2,64115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-17 kcal/mol
Surface area66410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.288, 244.937, 261.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 47 - 898 / Label seq-ID: 47 - 898

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Dipeptidyl peptidase 8 / / DP8 / Dipeptidyl peptidase IV-related protein 1 / DPRP-1 / Dipeptidyl peptidase VIII / DPP VIII / ...DP8 / Dipeptidyl peptidase IV-related protein 1 / DPRP-1 / Dipeptidyl peptidase VIII / DPP VIII / Prolyl dipeptidase DPP8


Mass: 103483.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6V1X1, dipeptidyl-peptidase IV
#2: Chemical
ChemComp-D06 / (2S)-2-amino-1-(1,3-dihydro-2H-isoindol-2-yl)-2-[(1r,4S)-4-(pyrrolidin-1-yl)cyclohexyl]ethan-1-one


Mass: 327.464 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C20H29N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H9NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.52 Å3/Da / Density % sol: 72.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.46 M NaCitrate pH 6.75

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 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: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.69→135.29 Å / Num. obs: 138235 / % possible obs: 96.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 1.97
Reflection shellResolution: 2.69→2.94 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.58 / Num. unique obs: 32528 / % possible all: 97.3

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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: 6EOO

6eoo


Resolution: 2.69→135.29 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 21.15 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.308 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 833 0.6 %RANDOM
Rwork0.1765 ---
obs0.1768 137401 96.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.15 Å2 / Biso mean: 64.883 Å2 / Biso min: 23.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å2-0 Å2-0 Å2
2--2.77 Å20 Å2
3----2.14 Å2
Refinement stepCycle: final / Resolution: 2.69→135.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20709 0 382 473 21564
Biso mean--100 50.33 -
Num. residues----2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01921416
X-RAY DIFFRACTIONr_bond_other_d0.0040.0219901
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.97329131
X-RAY DIFFRACTIONr_angle_other_deg1.308345778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2152555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18923.407995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115.2013559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.88215133
X-RAY DIFFRACTIONr_chiral_restr0.0950.23108
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02123972
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025061
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A204900.01
12B204900.01
21A203440.02
22C203440.02
31B202700.02
32C202700.02
LS refinement shellResolution: 2.69→2.76 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 53 -
Rwork0.463 10231 -
all-10284 -
obs--97.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.86680.0803-0.37341.7054-0.07910.72330.0519-0.05760.11930.09770.0338-0.0265-0.12410.068-0.08580.10850.03780.0210.2293-0.06290.0372-33.08431.41313.91
21.48850.1051-0.11991.37340.51781.33950.0663-0.06780.05560.141-0.03840.348-0.0461-0.2164-0.02790.03920.03580.06190.17530.04290.1205-59.06111.68414.259
31.5668-0.1789-0.20490.936-0.29420.86480.0686-0.11580.0995-0.02160.00610.0323-0.1679-0.149-0.07480.0878-0.01810.03730.3003-0.01830.0226-47.683-11.85157.15
41.0863-0.1436-0.56511.36350.31041.5046-0.0258-0.1106-0.32260.12360.00110.15470.2652-0.18970.02480.0574-0.0562-0.01640.22710.09520.1382-40.432-43.57956.945
51.5575-0.39760.21681.33480.32260.81290.0518-0.07740.04240.02920.0255-0.0923-0.01190.0986-0.07730.06930.00210.01230.1186-0.03320.01910.464-36.37431.437
61.5514-0.1263-0.38441.39990.30551.2734-0.00830.0566-0.3582-0.01520.01970.14250.258-0.099-0.01140.0811-0.0222-0.05020.0918-0.01810.1332-17.851-52.40429.106
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 626
2X-RAY DIFFRACTION2A627 - 898
3X-RAY DIFFRACTION3B47 - 626
4X-RAY DIFFRACTION4B627 - 898
5X-RAY DIFFRACTION5C47 - 626
6X-RAY DIFFRACTION6C627 - 898

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