[English] 日本語
Yorodumi
- PDB-9goc: Crystal structure of DPP9 Ser730Ala in complex with sulphostin. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9goc
TitleCrystal structure of DPP9 Ser730Ala in complex with sulphostin.
ComponentsDipeptidyl peptidase 9
KeywordsTRANSFERASE / Dipeptidyl peptidase / dipeptidyl peptidase inhibitor
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 / 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
: / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSewald, L. / Tabak, W.W.A. / Fehr, L. / Zolg, S. / Najdzion, M. / Verhoef, C.J.A. / Podlesainski, D. / Geiss-Friedlander, R. / Lammens, A. / Kaschani, F. ...Sewald, L. / Tabak, W.W.A. / Fehr, L. / Zolg, S. / Najdzion, M. / Verhoef, C.J.A. / Podlesainski, D. / Geiss-Friedlander, R. / Lammens, A. / Kaschani, F. / Hellerschmied, D. / Huber, R. / Kaiser, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1430, Project number 424228829 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors.
Authors: Sewald, L. / Tabak, W.W.A. / Fehr, L. / Zolg, S. / Najdzion, M. / Verhoef, C.J.A. / Podlesainski, D. / Geiss-Friedlander, R. / Lammens, A. / Kaschani, F. / Hellerschmied, D. / Huber, R. / Kaiser, M.
History
DepositionSep 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)394,57759
Polymers390,0304
Non-polymers4,54755
Water41,1282283
1
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,68835
Polymers195,0152
Non-polymers2,67333
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint84 kcal/mol
Surface area65860 Å2
MethodPISA
2
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,88924
Polymers195,0152
Non-polymers1,87422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint64 kcal/mol
Surface area66080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.613, 106.531, 121.270
Angle α, β, γ (deg.)65.15, 70.72, 76.35
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABCD

#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: 97507.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV

-
Non-polymers , 6 types, 2338 molecules

#2: Chemical
ChemComp-A1INE / Sulphostin / [azanyl-[(3~{S})-3-azanyl-2-oxidanylidene-piperidin-1-yl]phosphoryl]sulfamic acid


Mass: 272.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H13N4O5PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2283 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG2000 MME 20% (w/v), 0.1 M Tris pH 6.75

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 1.89→83.24 Å / Num. obs: 288843 / % possible obs: 96.2 % / Redundancy: 2.2 % / CC1/2: 0.99 / Net I/σ(I): 6
Reflection shellResolution: 1.89→1.93 Å / Num. unique obs: 14452 / CC1/2: 0.78

-
Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0267refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→83.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.551 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19945 2336 0.8 %RANDOM
Rwork0.17672 ---
obs0.17691 286483 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.475 Å2
Baniso -1Baniso -2Baniso -3
1-1.77 Å2-0.47 Å2-2.26 Å2
2---2.26 Å20.88 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.89→83.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27246 0 288 2283 29817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01328199
X-RAY DIFFRACTIONr_bond_other_d0.0030.01725803
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.64938266
X-RAY DIFFRACTIONr_angle_other_deg1.1631.57259472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25253428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.60522.1181497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3615.0134461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98415158
X-RAY DIFFRACTIONr_chiral_restr0.0590.23455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0231958
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026706
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9224.02713573
X-RAY DIFFRACTIONr_mcbond_other1.9214.02713572
X-RAY DIFFRACTIONr_mcangle_it3.136.03316984
X-RAY DIFFRACTIONr_mcangle_other3.1296.03316985
X-RAY DIFFRACTIONr_scbond_it2.1614.2114626
X-RAY DIFFRACTIONr_scbond_other2.1614.2114627
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5596.20721261
X-RAY DIFFRACTIONr_long_range_B_refined5.42345.01630122
X-RAY DIFFRACTIONr_long_range_B_other5.35344.74829745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A9895
12B9895
21A10042
22C10042
31A9871
32D9871
41B9832
42C9832
51B9758
52D9758
61C9812
62D9812
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 162 -
Rwork0.322 21095 -
obs--95.6 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more