9LBT | pdb_00009lbt

DPPIV-VAMP

• PDB DOI: https://doi.org/10.2210/pdb9LBT/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens, Cannabis sativa
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2025-01-03 Released: 2025-07-23 
• Deposition Author(s): Chen, H.H., Xing, X.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Discovery of an oral-admistrated biopeptide VAMP: a novel glucose homeostasis modulator with bifunctionalities of targeting intestinal DPP-IV and microbiota

Chen, H.H., Xing, X.H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 169.22 kDa 
• Atom Count: 13,431 
• Modeled Residue Count: 1,454 
• Deposited Residue Count: 1,460 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	726	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
PHAROS:  P27487 GTEx:  ENSG00000197635

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VAL-ALA-MET-PRO	C, D	4	Cannabis sativa	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.827	α = 90
b = 126.37	β = 90
c = 136.867	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-23 
Deposition Author(s): Chen, H.H., Xing, X.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32101936

Revision History  

• Version 1.0: 2025-07-23
  Type: Initial release