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- PDB-3n0t: Human dipeptidil peptidase DPP7 complexed with inhibitor GSK237826A -

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Basic information

Entry
Database: PDB / ID: 3n0t
TitleHuman dipeptidil peptidase DPP7 complexed with inhibitor GSK237826A
ComponentsDipeptidyl peptidase 2
KeywordsHYDROLASE / structural genomics / Structural Genomics Consortium / SGC / aminopeptidase / cleavage on pair of basic residues / cytoplasmic vesicle / glycoprotein / lysosome / protease / serine protease / zymogen
Function / homology
Function and homology information


dipeptidyl-peptidase II / lysosomal protein catabolic process / serine-type exopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / azurophil granule lumen / vesicle / intracellular membrane-bounded organelle / Neutrophil degranulation ...dipeptidyl-peptidase II / lysosomal protein catabolic process / serine-type exopeptidase activity / dipeptidyl-peptidase activity / aminopeptidase activity / serine-type peptidase activity / azurophil granule lumen / vesicle / intracellular membrane-bounded organelle / Neutrophil degranulation / Golgi apparatus / proteolysis / extracellular exosome / extracellular region
Similarity search - Function
Serine carboxypeptidase S28, SKS domain / Serine carboxypeptidase S28, SKS domain / Peptidase S28 / Serine carboxypeptidase S28 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...Serine carboxypeptidase S28, SKS domain / Serine carboxypeptidase S28, SKS domain / Peptidase S28 / Serine carboxypeptidase S28 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(3S)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine / Dipeptidyl peptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / Crombet, L. / Cossar, D. / Pagannon, S. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. ...Dobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / Crombet, L. / Cossar, D. / Pagannon, S. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hassell, A. / Shewchuk, L. / Haffner, C. / Bochkarev, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human dipeptidyl peptidase DPP7
Authors: Dobrovetsky, E. / Khutoreskaya, G. / Seitova, A. / Crombet, L. / Cossar, D. / Pagannon, S. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Hassell, A. / Shewchuk, L. / Haffner, C. / Bochkarev, A.
History
DepositionMay 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 2
B: Dipeptidyl peptidase 2
C: Dipeptidyl peptidase 2
D: Dipeptidyl peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,9148
Polymers208,1734
Non-polymers7414
Water4,468248
1
A: Dipeptidyl peptidase 2
B: Dipeptidyl peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4574
Polymers104,0872
Non-polymers3712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-10 kcal/mol
Surface area31550 Å2
MethodPISA
2
C: Dipeptidyl peptidase 2
D: Dipeptidyl peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4574
Polymers104,0872
Non-polymers3712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-11 kcal/mol
Surface area31160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.546, 130.500, 125.075
Angle α, β, γ (deg.)90.00, 102.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dipeptidyl peptidase 2 / / Dipeptidyl peptidase II / DPP II / Dipeptidyl aminopeptidase II / Quiescent cell proline ...Dipeptidyl peptidase II / DPP II / Dipeptidyl aminopeptidase II / Quiescent cell proline dipeptidase / Dipeptidyl peptidase 7


Mass: 52043.344 Da / Num. of mol.: 4 / Fragment: Peptidase domain (UNP residues 28-492)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP2, DPP7, QPP / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UHL4, dipeptidyl-peptidase II
#2: Chemical
ChemComp-OPY / (3S)-4-oxo-4-piperidin-1-ylbutane-1,3-diamine / GSK237826A


Mass: 185.267 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H19N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 60.13 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2M AMMONIUM SULFATE, 0.2M SODIUM ACETATE, 0.1M HEPES, 5% MPD, PH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→122.213 Å / Num. obs: 92014 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 50.34 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.45-2.493.10.79399.7
2.49-2.543.10.74899.8
2.54-2.593.10.66699.9
2.59-2.643.10.58299.8
2.64-2.73.10.50899.9
2.7-2.763.20.44499.9
2.76-2.833.20.40999.8
2.83-2.93.20.35499.8
2.9-2.993.20.29999.8
2.99-3.083.20.26199.8
3.08-3.193.20.21499.7
3.19-3.323.20.16699.7
3.32-3.473.20.12699.5
3.47-3.653.20.10298.8
3.65-3.883.30.08398.7
3.88-4.183.30.06998.8
4.18-4.63.40.05798.7
4.6-5.253.50.05599.2
5.25-6.573.60.05999.8
6.57-203.70.04399.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
MOLREPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3JYH

3jyh


Resolution: 2.45→20.01 Å / Cor.coef. Fo:Fc: 0.8987 / Cor.coef. Fo:Fc free: 0.8616 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 4609 5.01 %RANDOM
Rwork0.2185 ---
obs0.2206 91963 --
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.9067 Å20 Å2-4.9363 Å2
2---2.652 Å20 Å2
3---0.7453 Å2
Refine analyzeLuzzati coordinate error obs: 0.361 Å
Refinement stepCycle: LAST / Resolution: 2.45→20.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13833 0 52 248 14133
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0719476HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4565SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes313HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2169HARMONIC5
X-RAY DIFFRACTIONt_it14241HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.75
X-RAY DIFFRACTIONt_other_torsion17.74
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion18845
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact167794
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3102 350 5.24 %
Rwork0.2498 6324 -
all0.253 6674 -
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)
10.3572-0.19960.05740.7273-0.360.9603-0.0603-0.010.01370.04140.0153-0.09710.0403-0.02070.045-0.0604-0.0072-0.0841-0.1058-0.0175-0.0107-19.47640.216414.7866
20.4740.1860.00140.5665-0.330.7845-0.06090.0103-0.0162-0.01990.043-0.0549-0.032-0.02570.0179-0.03250.0042-0.0698-0.1183-0.0275-0.0121-19.377634.0102-14.3854
30.8979-0.40250.63010.8973-0.59161.09210.0142-0.14460.147-0.13270.0363-0.02130.0235-0.0974-0.05050.0183-0.0684-0.0962-0.1164-0.0332-0.10972.860920.423265.398
41.131-0.59640.5661.0245-0.24470.67270.0325-0.0878-0.0527-0.12210.0689-0.03130.2604-0.0905-0.10140.0856-0.0755-0.0837-0.1147-0.0258-0.173124.418-13.417384.9288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|1 A|28 - A|479 A|493 - A|498 A|1001 - A|1001 }A1
2X-RAY DIFFRACTION1{ A|1 - A|1 A|28 - A|479 A|493 - A|498 A|1001 - A|1001 }A28 - 479
3X-RAY DIFFRACTION1{ A|1 - A|1 A|28 - A|479 A|493 - A|498 A|1001 - A|1001 }A493 - 498
4X-RAY DIFFRACTION1{ A|1 - A|1 A|28 - A|479 A|493 - A|498 A|1001 - A|1001 }A1001
5X-RAY DIFFRACTION2{ B|1 - B|1 B|28 - B|479 B|493 - B|497 B|1001 - B|1001 }B1
6X-RAY DIFFRACTION2{ B|1 - B|1 B|28 - B|479 B|493 - B|497 B|1001 - B|1001 }B28 - 479
7X-RAY DIFFRACTION2{ B|1 - B|1 B|28 - B|479 B|493 - B|497 B|1001 - B|1001 }B493 - 497
8X-RAY DIFFRACTION2{ B|1 - B|1 B|28 - B|479 B|493 - B|497 B|1001 - B|1001 }B1001
9X-RAY DIFFRACTION3{ C|1 - C|1 C|28 - C|478 C|493 - C|498 C|1001 - C|1001 }A1 - 499
10X-RAY DIFFRACTION3{ C|1 - C|1 C|28 - C|478 C|493 - C|498 C|1001 - C|1001 }C28 - 478
11X-RAY DIFFRACTION3{ C|1 - C|1 C|28 - C|478 C|493 - C|498 C|1001 - C|1001 }C493 - 498
12X-RAY DIFFRACTION3{ C|1 - C|1 C|28 - C|478 C|493 - C|498 C|1001 - C|1001 }C1001
13X-RAY DIFFRACTION4{ D|1 - D|1 D|29 - D|477 D|493 - D|496 D|1001 - D|1001 }D1
14X-RAY DIFFRACTION4{ D|1 - D|1 D|29 - D|477 D|493 - D|496 D|1001 - D|1001 }D29 - 477
15X-RAY DIFFRACTION4{ D|1 - D|1 D|29 - D|477 D|493 - D|496 D|1001 - D|1001 }D493 - 496
16X-RAY DIFFRACTION4{ D|1 - D|1 D|29 - D|477 D|493 - D|496 D|1001 - D|1001 }D1001

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