7C92 | pdb_00007c92

Structure of Serratia marcescens chitinase B complexed with compound 6k

• PDB DOI: https://doi.org/10.2210/pdb7C92/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-04 Released: 2021-06-09 
• Deposition Author(s): Jiang, X., Yuan, P.T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 
  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Discovery of novel Chitinase Inhibitors with a scaffold of dipyridopyrimidine-3-carboxamide via Structure-based Rational Design

Yuan, P.T., Jiang, X.

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 and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 114.6 kDa 
• Atom Count: 8,325 
• Modeled Residue Count: 990 
• Deposited Residue Count: 1,018 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase	A, B	509	Serratia marcescens	Mutation(s): 0  Gene Names: chiB EC: 3.2.1.14
UniProt
Find proteins for P11797 (Serratia marcescens) Explore P11797  Go to UniProtKB:  P11797

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FXR (Subject of Investigation/LOI)	C [auth A], D [auth B], E [auth B]	6-azanyl-11-methyl-2-oxidanylidene-N-(pyridin-3-ylmethyl)-1,7,9-triazatricyclo[8.4.0.0^3,8]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide C19 H16 N6 O2 FDRSMDXOIMNVLE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free:  0.230 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.362	α = 90
b = 103.644	β = 90
c = 186.792	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Jiang, X., Yuan, P.T.

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary