[English] 日本語
Yorodumi
- PDB-2gbg: rat DPP-IV with alkynyl cyanopyrrolidine #2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gbg
Titlerat DPP-IV with alkynyl cyanopyrrolidine #2
ComponentsDipeptidyl peptidase 4
KeywordsHYDROLASE / serine peptidase beta propeller
Function / homology
Function and homology information


B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / positive regulation of natural killer cell mediated immunity / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus ...B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / positive regulation of natural killer cell mediated immunity / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / collagen binding / T cell costimulation / serine-type peptidase activity / T cell activation / peptide binding / protein catabolic process / lamellipodium / virus receptor activity / protease binding / response to hypoxia / cell adhesion / membrane raft / apical plasma membrane / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region ...Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / 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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1AD / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLongenecker, K.L. / Jakob, C.G. / Fry, E.H. / Wilk, S.
CitationJournal: Biochemistry / Year: 2006
Title: Crystal Structures of DPP-IV (CD26) from Rat Kidney Exhibit Flexible Accommodation of Peptidase-Selective Inhibitors.
Authors: Longenecker, K.L. / Stewart, K.D. / Madar, D.J. / Jakob, C.G. / Fry, E.H. / Wilk, S. / Lin, C.W. / Ballaron, S.J. / Stashko, M.A. / Lubben, T.H. / Yong, H. / Pireh, D. / Pei, Z. / Basha, F. ...Authors: Longenecker, K.L. / Stewart, K.D. / Madar, D.J. / Jakob, C.G. / Fry, E.H. / Wilk, S. / Lin, C.W. / Ballaron, S.J. / Stashko, M.A. / Lubben, T.H. / Yong, H. / Pireh, D. / Pei, Z. / Basha, F. / Wiedeman, P.E. / Von Geldern, T.W. / Trevillyan, J.M. / Stoll, V.S.
History
DepositionMar 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,0354
Polymers168,6752
Non-polymers3592
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-32 kcal/mol
Surface area56670 Å2
MethodPISA
2
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules

A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules

A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,10412
Polymers506,0256
Non-polymers1,0786
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area22360 Å2
ΔGint-145 kcal/mol
Surface area162750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.500, 207.500, 207.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Detailsdimer of asymmetric unit is thought to be biologically relevant

-
Components

#1: Protein Dipeptidyl peptidase 4


Mass: 84337.578 Da / Num. of mol.: 2
Fragment: Dipeptidyl Peptidase 4 Soluble Form (Residues 38-767)
Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P14740, dipeptidyl-peptidase IV
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1AD / (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-PROP-1-YN-1-YLPYRROLIDIN-1-YL]-1-CYCLOPENTYL-2-OXOETHANAMINE


Mass: 263.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N3O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 72.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 2.8 M ammonium sulfate and 100mM sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 59362 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.106 / Χ2: 1.097 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
3-3.1199.46.40.68858710.817
3.11-3.2399.66.70.4658890.867
3.23-3.3899.76.80.33758940.882
3.38-3.5699.770.23159100.953
3.56-3.7899.97.10.16159661.009
3.78-4.0799.97.20.11859641.074
4.07-4.4899.87.30.08259041.167
4.48-5.1399.57.40.06559531.252
5.13-6.4699.27.50.06259991.156
6.46-5097.27.40.04560121.676

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 2997 5 %
Rwork0.235 --
obs-59077 99.4 %
Displacement parametersBiso mean: 57.058 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11840 0 24 0 11864
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_repADD.param
X-RAY DIFFRACTION2add.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.param

+
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