[English] 日本語
Yorodumi
- PDB-7zxs: Crystal structure of DPP9 in complex with a 4-oxo-b-lactam based ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zxs
TitleCrystal structure of DPP9 in complex with a 4-oxo-b-lactam based inhibitor, A295
Components(Dipeptidyl peptidase ...) x 2
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE / DPP9
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 / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 8 Propeller / Methanol Dehydrogenase; Chain A / 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 / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 8 Propeller / Methanol Dehydrogenase; Chain A / 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-KBO / DI(HYDROXYETHYL)ETHER / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsRoss, B. / Huber, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Chemoproteomics-Enabled Identification of 4-Oxo-beta-Lactams as Inhibitors of Dipeptidyl Peptidases 8 and 9.
Authors: Carvalho, L.A.R. / Ross, B. / Fehr, L. / Bolgi, O. / Wohrle, S. / Lum, K.M. / Podlesainski, D. / Vieira, A.C. / Kiefersauer, R. / Felix, R. / Rodrigues, T. / Lucas, S.D. / Gross, O. / Geiss- ...Authors: Carvalho, L.A.R. / Ross, B. / Fehr, L. / Bolgi, O. / Wohrle, S. / Lum, K.M. / Podlesainski, D. / Vieira, A.C. / Kiefersauer, R. / Felix, R. / Rodrigues, T. / Lucas, S.D. / Gross, O. / Geiss-Friedlander, R. / Cravatt, B.F. / Huber, R. / Kaiser, M. / Moreira, R.
History
DepositionMay 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
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)394,29952
Polymers389,6014
Non-polymers4,69848
Water29,7791653
1
A: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,89522
Polymers194,8172
Non-polymers2,07820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,40430
Polymers194,7852
Non-polymers2,61928
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.350, 106.176, 121.127
Angle α, β, γ (deg.)65.250, 70.430, 75.860
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA22 - 8653 - 846
21BB22 - 8653 - 846
12AA22 - 8653 - 846
22CC22 - 8653 - 846
13AA22 - 8653 - 846
23DD22 - 8653 - 846
14BB21 - 8652 - 846
24CC21 - 8652 - 846
15BB22 - 8643 - 845
25DD22 - 8643 - 845
16CC22 - 8653 - 846
26DD22 - 8653 - 846

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Dipeptidyl peptidase ... , 2 types, 4 molecules ACBD

#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: 97408.328 Da / Num. of mol.: 2 / Fragment: extcolor{red}{>FRAGMENT<}
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: 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: 97392.328 Da / Num. of mol.: 2
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

-
Non-polymers , 4 types, 1701 molecules

#3: Chemical
ChemComp-KBO / 2-ethyl-2-methanoyl-~{N}-[3-[[4-(quinolin-8-ylmethyl)piperazin-1-yl]methyl]phenyl]butanamide


Mass: 458.595 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H34N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1653 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystal is grown in a condition containing PEG 2K MME buffered by Tris pH 7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.807→106.9 Å / Num. obs: 220955 / % possible obs: 64.6 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 5.4
Reflection shellResolution: 1.807→1.955 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 11048 / Rsym value: 0.459 / % possible all: 15.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
X-GENdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOR

6eor


Resolution: 1.81→106.09 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.678 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 1707 0.8 %RANDOM
Rwork0.1752 ---
obs0.1754 219248 64.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.39 Å2 / Biso mean: 34.669 Å2 / Biso min: 16.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20.07 Å2-0.02 Å2
2---0.04 Å2-0.06 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.81→106.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27210 0 281 1653 29144
Biso mean--47.4 39.52 -
Num. residues----3364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01327958
X-RAY DIFFRACTIONr_bond_other_d0.0020.01725440
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.64937983
X-RAY DIFFRACTIONr_angle_other_deg1.1911.57358559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18853417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95522.1471439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.978154295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.17915147
X-RAY DIFFRACTIONr_chiral_restr0.0610.23454
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231833
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026645
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A97910.03
12B97910.03
21A97650.03
22C97650.03
31A96960.03
32D96960.03
41B98450.03
42C98450.03
51B97900.03
52D97900.03
61C98170.02
62D98170.02
LS refinement shellResolution: 1.81→1.854 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 10 -
Rwork0.284 1059 -
obs--4.22 %

+
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