8GRT | pdb_00008grt

Small Dipeptide Analogues developed by Co-crystal Structure of Stenotrophomonas maltophilia Dipeptidyl Peptidase 7

• PDB DOI: https://doi.org/10.2210/pdb8GRT/pdb

• Classification: HYDROLASE
• Organism(s): Stenotrophomonas maltophilia R551-3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-02 Released: 2023-09-06 
• Deposition Author(s): Yasumitsu, S., Koushi, H., Akihiro, N., Yoshiyuki, Y., Wataru, O., Mizuki, S., Saori, R., Nobutada, T., Anna, M., Keiko, H., Tsuda, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 

Literature

Small Dipeptide Analogues Generated by Co-crystal Structure of Bacterial Dipeptidyl Peptidase 7 to Defeat Stenotrophomonas maltophilia

Koushi, H., Yasumitsu, S., Akihiro, N., Suzuki, Y., Wataru, O., Mizuki, S., Chisato, K., Saori, R., Nobutada, T., Anna, M., Keiko, H., Yuko, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 156.83 kDa 
• Atom Count: 10,908 
• Modeled Residue Count: 1,393 
• Deposited Residue Count: 1,440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl-peptidase	A, B	720	Stenotrophomonas maltophilia R551-3	Mutation(s): 0  Gene Names: Smal_0807 EC: 3.4.14
UniProt
Find proteins for B4SLK2 (Stenotrophomonas maltophilia (strain R551-3)) Explore B4SLK2  Go to UniProtKB:  B4SLK2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYR	D [auth A], F [auth B]	TYROSINE C9 H11 N O3 OUYCCCASQSFEME-QMMMGPOBSA-N
ALC (Subject of Investigation/LOI)	C [auth A], E [auth B]	2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID C9 H17 N O2 ORQXBVXKBGUSBA-QMMMGPOBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.2	α = 90
b = 74.25	β = 95.11
c = 154.59	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
xia2	data reduction
DIALS	data reduction
PHASER	phasing
REFMAC	refinement
Coot	model building
BUCCANEER	model building
PHENIX	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-06 
Deposition Author(s): Yasumitsu, S., Koushi, H., Akihiro, N., Yoshiyuki, Y., Wataru, O., Mizuki, S., Saori, R., Nobutada, T., Anna, M., Keiko, H., Tsuda, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	16K8322
Japan Society for the Promotion of Science (JSPS)	Japan	16H04902
Japan Society for the Promotion of Science (JSPS)	Japan	17H03790
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	2013A6822, 2013B6822, 2014A6924, 2014B6924, 2015A6521, 2015B6521, 2016B6620, 2017A6721, 2017B6721, 2018A6818, 2018B6818, 2019A6917, 2019B6917, 2020A6517
Japan Agency for Medical Research and Development (AMED)	Japan	BINDS 0026
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21K09913
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21K06071

Revision History  

• Version 1.0: 2023-09-06
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary