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- PDB-9lbt: DPPIV-VAMP -

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Basic information

Entry
Database: PDB / ID: 9lbt
TitleDPPIV-VAMP
Components
  • Dipeptidyl peptidase 4 soluble form
  • VAL-ALA-MET-PRO
KeywordsPEPTIDE BINDING PROTEIN / DPP-IV / VAMP
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 / T cell costimulation / receptor-mediated endocytosis of virus by host cell / 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
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
Similarity search - Domain/homology
Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Cannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsChen, H.H. / Xing, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32101936 China
CitationJournal: To Be Published
Title: Discovery of an oral-admistrated biopeptide VAMP: a novel glucose homeostasis modulator with bifunctionalities of targeting intestinal DPP-IV and microbiota
Authors: Chen, H.H. / Xing, X.H.
History
DepositionJan 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 4 soluble form
B: Dipeptidyl peptidase 4 soluble form
C: VAL-ALA-MET-PRO
D: VAL-ALA-MET-PRO


Theoretical massNumber of molelcules
Total (without water)169,2184
Polymers169,2184
Non-polymers00
Water27,7971543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-27 kcal/mol
Surface area56880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.827, 126.370, 136.867
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dipeptidyl peptidase 4 soluble form / Dipeptidyl peptidase IV soluble form


Mass: 84192.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: unidentified baculovirus / References: UniProt: P27487
#2: Protein/peptide VAL-ALA-MET-PRO


Mass: 416.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Cannabis sativa (plant)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1543 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.33 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.25 M Ammonium acetate, 0.1 M Tris pH 8.5, 21% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.99→32.41 Å / Num. obs: 138319 / % possible obs: 98.69 % / Redundancy: 11.6 % / Rpim(I) all: 0.037 / Net I/σ(I): 14.93
Reflection shellResolution: 1.99→2.06 Å / Num. unique obs: 138311 / Rpim(I) all: 0.037

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→32.41 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 2003 1.45 %
Rwork0.1687 --
obs0.1691 138313 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11888 0 0 1543 13431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d6.8621618
X-RAY DIFFRACTIONf_chiral_restr0.0831756
X-RAY DIFFRACTIONf_plane_restr0.0132110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.34531200.2538920X-RAY DIFFRACTION91
2.04-2.090.24921560.21279582X-RAY DIFFRACTION98
2.09-2.160.24351460.18859608X-RAY DIFFRACTION98
2.16-2.230.22781330.17899648X-RAY DIFFRACTION98
2.23-2.310.20251470.17649663X-RAY DIFFRACTION99
2.31-2.40.20251400.16659710X-RAY DIFFRACTION99
2.4-2.510.19621500.16449713X-RAY DIFFRACTION99
2.51-2.640.22581430.16989735X-RAY DIFFRACTION99
2.64-2.80.22511390.16979792X-RAY DIFFRACTION99
2.8-3.020.19541450.17179851X-RAY DIFFRACTION100
3.02-3.320.20051470.16399861X-RAY DIFFRACTION100
3.32-3.80.17771400.1569934X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6127-0.23880.03050.28410.2390.39360.16360.1535-0.289-0.0462-0.08390.08450.31060.0079-0.02930.3441-0.0153-0.00510.26140.01030.2985-8.0528-6.2919-55.0338
21.1272-0.01990.09710.30260.03270.51540.0873-0.2077-0.35820.0448-0.0386-0.07410.14870.0198-0.00950.2331-0.0059-0.04130.17470.08440.2833-14.3526-8.1162-28.4658
31.47640.1910.1510.56270.10120.67120.0163-0.2627-0.00460.1277-0.0435-0.0619-0.05570.1242-0.00690.1794-0.0069-0.03120.19120.01160.18061.199313.4422-28.6936
41.466-0.23720.24110.4443-0.12820.8581-0.01640.23070.1721-0.0269-0.0383-0.0627-0.10470.09820.01460.2088-0.03480.0040.19930.04210.1669-4.098515.7446-55.4596
50.98650.09740.06720.3910.10.5635-0.03050.09440.22-0.01380.03060.0112-0.173-0.04260.01170.20440.0139-0.00230.15070.02940.2072-23.781524.4714-46.7476
61.16730.17050.04030.68240.05480.6912-0.0011-0.00910.12550.01310.00160.0712-0.0825-0.07810.00530.14220.0180.01030.11630.01650.1478-33.735216.4834-38.816
70.7972-0.0322-0.0860.4161-0.1910.44610.2022-0.27860.32980.2939-0.12-0.2167-0.38410.21540.02660.3172-0.034-0.04680.2425-0.01590.3603-75.941222.9238-24.3147
80.95390.3496-0.46260.3951-0.33530.94010.0738-0.08340.09440.105-0.0423-0.023-0.142-0.06080.04070.19110.0011-0.02310.16890.010.161-62.7161.0759-13.378
91.01450.1173-0.19730.3148-0.03990.29320.00080.18770.0149-0.05760.01390.02830.0355-0.0776-0.00870.1345-0.0038-0.02670.1720.00890.1341-71.16640.7886-40.6957
100.142-0.07610.1320.3136-0.00940.13630.04960.0126-0.1394-0.08730.05460.01410.08990.0035-0.06160.4421-0.01190.08780.9406-0.07670.5561-21.845511.9388-39.5546
111.17151.2511-0.6884.38880.08770.62550.07170.12490.1001-0.09260.00750.2216-0.0694-0.1322-0.06140.30860.03980.10360.36960.08650.5491-62.44342.4361-37.0719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 255 )
3X-RAY DIFFRACTION3chain 'A' and (resid 256 through 387 )
4X-RAY DIFFRACTION4chain 'A' and (resid 388 through 499 )
5X-RAY DIFFRACTION5chain 'A' and (resid 500 through 616 )
6X-RAY DIFFRACTION6chain 'A' and (resid 617 through 723 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 59 )
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 255 )
9X-RAY DIFFRACTION9chain 'B' and (resid 256 through 723 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 4 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 4 )

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