[English] 日本語
Yorodumi
- PDB-7svn: DPP9 IN COMPLEX WITH LIGAND ICeD-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7svn
TitleDPP9 IN COMPLEX WITH LIGAND ICeD-1
ComponentsDipeptidyl peptidase 9
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE
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-CW8 / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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
Revision 1.2Oct 30, 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)397,8668
Polymers396,8534
Non-polymers1,0134
Water9,854547
1
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,9334
Polymers198,4262
Non-polymers5072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-14 kcal/mol
Surface area66370 Å2
MethodPISA
2
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,9334
Polymers198,4262
Non-polymers5072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-16 kcal/mol
Surface area66130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.789, 117.439, 163.455
Angle α, β, γ (deg.)90.000, 105.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEUAA20 - 86320 - 863
21PROPROLEULEUBB20 - 86320 - 863
12PROPROHISHISAA20 - 86420 - 864
22PROPROHISHISCC20 - 86420 - 864
13ASPASPHISHISAA19 - 86419 - 864
23ASPASPHISHISDD19 - 86419 - 864
14PROPROLEULEUBB20 - 86320 - 863
24PROPROLEULEUCC20 - 86320 - 863
15PROPROLEULEUBB20 - 86320 - 863
25PROPROLEULEUDD20 - 86320 - 863
16PROPROHISHISCC20 - 86420 - 864
26PROPROHISHISDD20 - 86420 - 864

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#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: 99213.211 Da / Num. of mol.: 4
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: Chemical
ChemComp-CW8 / (2S,4S)-1-[(2S)-2-amino-2-cyclohexylacetyl]-4-fluoropyrrolidine-2-carbonitrile


Mass: 253.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H20FN3O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 10% PEG 8000 25% glycerol 0.16 M calcium acetate 0.08 M cacodilate pH 6.25

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9999 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: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.78→157.52 Å / Num. obs: 103766 / % possible obs: 94.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 1.92
Reflection shellResolution: 2.78→3.03 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.593 / Num. unique obs: 23973 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EOQ

6eoq


Resolution: 2.78→157.52 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.824 / SU B: 23.704 / SU ML: 0.446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3489 732 0.7 %RANDOM
Rwork0.267 ---
obs0.2675 103032 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 229.61 Å2 / Biso mean: 42.485 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.52 Å2-0 Å2-0.07 Å2
2--2.58 Å20 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.78→157.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26773 0 72 547 27392
Biso mean--44.65 21.1 -
Num. residues----3303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01927079
X-RAY DIFFRACTIONr_bond_other_d0.0040.0224788
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.94236843
X-RAY DIFFRACTIONr_angle_other_deg1.223356862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3553291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04823.321259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1715.0674207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.67115147
X-RAY DIFFRACTIONr_chiral_restr0.090.23900
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02130758
X-RAY DIFFRACTIONr_gen_planes_other0.0020.026621
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.02 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A18542
12B18542
21A18442
22C18442
31A18730
32D18730
41B18706
42C18706
51B18632
52D18632
61C18778
62D18778
LS refinement shellResolution: 2.78→2.852 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 58 -
Rwork0.403 7747 -
all-7805 -
obs--96.74 %

+
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