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- PDB-6rn6: DPP1 in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 6rn6
TitleDPP1 in complex with inhibitor
Components(Dipeptidyl peptidase ...) x 3
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE I / INHIBITOR COMPLEX / Cathepsin C
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / : / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / : / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Lipocalin / Papain-like cysteine peptidase superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-K9Q / Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKack, H.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: DPP1 Inhibitors: Exploring the Role of Water in the S2 Pocket of DPP1 with Substituted Pyrrolidines.
Authors: Kack, H. / Doyle, K. / Hughes, S.J. / Bodnarchuk, M.S. / Lonn, H. / Van De Poel, A. / Palmer, N.
History
DepositionMay 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 1
B: Dipeptidyl peptidase 1
C: Dipeptidyl peptidase 1
D: Dipeptidyl peptidase 1
E: Dipeptidyl peptidase 1
F: Dipeptidyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,18716
Polymers78,9156
Non-polymers1,27210
Water4,089227
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21400 Å2
ΔGint-168 kcal/mol
Surface area27670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.591, 84.591, 223.385
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121

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Components

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Dipeptidyl peptidase ... , 3 types, 6 molecules ADBECF

#1: Protein Dipeptidyl peptidase 1 / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPPI / Dipeptidyl transferase


Mass: 13500.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein Dipeptidyl peptidase 1 / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPPI / Dipeptidyl transferase


Mass: 18373.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein Dipeptidyl peptidase 1 / Cathepsin C / Cathepsin J / Dipeptidyl peptidase I / DPPI / Dipeptidyl transferase


Mass: 7583.444 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 1 types, 3 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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 , 4 types, 234 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-K9Q / (2~{S},4~{R})-~{N}-[(2~{S})-1-azanyl-3-(4-phenylphenyl)propan-2-yl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 339.431 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 3350, 0.2 M Ammoniumsulphate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→74.5 Å / Num. obs: 36889 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.3
Reflection shellResolution: 2.4→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1786 / CC1/2: 0.704 / % possible all: 95.6

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K3B

1k3b


Resolution: 2.4→14.87 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.272 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.282 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.21
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1824 -RANDOM
Rwork0.174 ---
obs0.176 36554 98.9 %-
Displacement parametersBiso mean: 52.83 Å2
Baniso -1Baniso -2Baniso -3
1--6.1683 Å20 Å20 Å2
2---6.1683 Å20 Å2
3---12.3366 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5450 0 78 227 5755
LS refinement shellHighest resolution: 2.4 Å
Refinement TLS params.

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)
11.84410.10980.18521.7746-0.28381.8334-0.18740.1783-0.4690.17830.1065-0.2762-0.469-0.27620.0809-0.04750.1383-0.0696-0.05840.0330.0074-32.1804-1.8154-1.7157
22.193-0.17780.49331.3647-0.28771.165-0.02020.05640.07060.05640.1021-0.30770.0706-0.3077-0.0819-0.16810.03880.0118-0.00350.06690.0247-40.3902-25.42620.56
31.31690.0012-0.02941.8949-0.22351.6907-0.044-0.23490.1794-0.23490.1212-0.15860.1794-0.1586-0.0772-0.16540.0227-0.02850.0234-0.01060.0978-39.077-29.6224-9.7286
42.6693-0.08721.00192.6423-0.1722.1428-0.18950.33920.01690.33920.161-0.43240.0169-0.43240.02850.01610.13670.03030.04860.0607-0.1787-19.5397-25.750226.6003
51.8365-0.35541.25132.45220.37171.7947-0.32850.3905-0.40980.39050.1257-0.0735-0.4098-0.07350.20280.03990.132-0.1363-0.1643-0.0679-0.0547-8.534-3.728621.6563
62.9033-0.01632.25011.5062-0.14252.2574-0.3750.2351-0.4350.23510.07520.152-0.4350.1520.29980.010.0727-0.1601-0.1496-0.02660.04242.0598-6.41720.4194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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