[English] 日本語
Yorodumi
- PDB-1nu6: Crystal structure of human Dipeptidyl Peptidase IV (DPP-IV) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nu6
TitleCrystal structure of human Dipeptidyl Peptidase IV (DPP-IV)
ComponentsDipeptidyl peptidase IV
KeywordsHYDROLASE / exopeptidase / beta barrel / alpha/beta hydrolase fold / DPP-IV
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / chemorepellent activity / psychomotor behavior / intercellular canaliculus / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / chemorepellent activity / psychomotor behavior / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / receptor-mediated endocytosis of virus by host cell / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / membrane fusion / response to hypoxia / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / membrane raft / symbiont entry into host cell / signaling receptor binding / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / 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 ...Dipeptidylpeptidase IV, N-terminal domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / 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
: / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsHennig, M. / Stihle, M. / Thoma, R. / Ruf, A.
CitationJournal: Structure / Year: 2003
Title: Structural Basis of Proline-Specific Exopeptidase Activity as Observed in Human Dipeptidyl Peptidase-IV.
Authors: Thoma, R. / Loeffler, B. / Stihle, M. / Huber, W. / Ruf, A. / Hennig, M.
History
DepositionJan 31, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 23, 2014Group: Experimental preparation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,89816
Polymers168,9252
Non-polymers2,97314
Water5,801322
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-93 kcal/mol
Surface area59950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.496, 68.240, 419.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Dipeptidyl peptidase IV / DPP IV


Mass: 84462.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcHDP1-23 / Production host: Pichia pastoris (fungus) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
220-25 %PEG33501reservoir
3200 mM1reservoirMgCl2
515 %glycerol1reservoir
4Tris1reservoirpH8.5

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2001 / Details: mirrors
RadiationMonochromator: mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.1→12 Å / Num. all: 234528 / Num. obs: 87113 / % possible obs: 82.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.2 Å / Rmerge(I) obs: 0.268 / % possible all: 72.3
Reflection
*PLUS
Num. measured all: 234528 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 72.3 %

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→12 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.427 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.28 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 4619 5 %RANDOM
Rwork0.21485 ---
all0.2174 87113 --
obs0.21747 87113 82.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.635 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2--4.24 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11926 0 118 322 12366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02112400
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210588
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.93616876
X-RAY DIFFRACTIONr_angle_other_deg0.889324632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.18331454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.35152075
X-RAY DIFFRACTIONr_chiral_restr0.1350.21790
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213738
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022674
X-RAY DIFFRACTIONr_nbd_refined0.240.32592
X-RAY DIFFRACTIONr_nbd_other0.2230.310721
X-RAY DIFFRACTIONr_nbtor_other0.4940.517
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.5820
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1150.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2770.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3970.53
X-RAY DIFFRACTIONr_mcbond_it0.8741.57252
X-RAY DIFFRACTIONr_mcangle_it1.603211766
X-RAY DIFFRACTIONr_scbond_it2.335148
X-RAY DIFFRACTIONr_scangle_it3.6384.55110
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 91
Rwork0.246 2014
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.86

+
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