5SDJ | pdb_00005sdj

PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z32327641

• PDB DOI: https://doi.org/10.2210/pdb5SDJ/pdb
• Deposition Group: G_1002227 (changed state) | Explore  G_1002227  

• Classification: HYDROLASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-20 Released: 2022-02-09 
• Deposition Author(s): Tham, C.T., Coker, J.A., Krojer, T., Foster, W.R., Koekemoer, L., Douangamath, A., Talon, R., Fearon, D., von Delft, F., Yue, W.W., Bountra, C., Bezerra, G.A.
• Funding Organization(s): University of Oxford

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Tham, C.T., Coker, J.A., Krojer, T., Foster, W.R., Koekemoer, L., Douangamath, A., Talon, R., Fearon, D., von Delft, F., Yue, W.W., Bountra, C., Bezerra, G.A.

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.

Macromolecule Content 

• Total Structure Weight: 161.86 kDa 
• Atom Count: 11,238 
• Modeled Residue Count: 1,392 
• Deposited Residue Count: 1,414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asp/Glu-specific dipeptidyl-peptidase	A, B	707	Porphyromonas gingivalis	Mutation(s): 0  Gene Names: dpp11, PGN_0607 EC: 3.4.14
UniProt
Find proteins for B2RID1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RID1  Go to UniProtKB:  B2RID1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
JMM (Subject of Investigation/LOI)	C [auth A]	[4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone C13 H16 N2 O3 SMBREKYBPARCFW-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.73	α = 90
b = 117.072	β = 90
c = 147.724	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Tham, C.T., Coker, J.A., Krojer, T., Foster, W.R., Koekemoer, L., Douangamath, A., Talon, R., Fearon, D., von Delft, F., Yue, W.W., Bountra, C., Bezerra, G.A.

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Funding Organization	Location	Grant Number
University of Oxford	United Kingdom	0006369

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.2: 2026-02-18
  Changes: Refinement description