7XNM | pdb_00007xnm

Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex

• PDB DOI: https://doi.org/10.2210/pdb7XNM/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa, Magallana gigas
• Mutation(s): No 


• Deposited: 2022-04-29 Released: 2023-05-17 
• Deposition Author(s): Li, W.Y., Cao, M.J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free: 
  0.299 (Depositor), 0.295 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structure of porcine dipeptidyl peptidase 4 inhibitory peptide complex

Li, W.Y., Cao, M.J.

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)

Macromolecule Content 

• Total Structure Weight: 174.41 kDa 
• Atom Count: 12,227 
• Modeled Residue Count: 1,467 
• Deposited Residue Count: 1,470 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	728	Sus scrofa	Mutation(s): 0  EC: 3.4.14.5
UniProt
Find proteins for P22411 (Sus scrofa) Explore P22411  Go to UniProtKB:  P22411
Glycosylation
Glycosylation Sites: 5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ILE-LEU-ALA-PRO-PRO-GLU-ARG	C, D	7	Magallana gigas	Mutation(s): 0

Oligosaccharides

Help  

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J, K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	L [auth A], M [auth A], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.58 Å
• R-Value Free:  0.299 (Depositor), 0.295 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 257.34	α = 90
b = 75.617	β = 110.199
c = 121.679	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-17 
Deposition Author(s): Li, W.Y., Cao, M.J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary