7CB1 | pdb_00007cb1

Structure of Serratia marcescens chitinase B complexed with compound 6q

• PDB DOI: https://doi.org/10.2210/pdb7CB1/pdb

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


• Deposited: 2020-06-10 Released: 2021-06-16 
• Deposition Author(s): Jiang, X., Yuan, P.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

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

Jiang, X., Yuan, P.T.

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: 114.82 kDa 
• Atom Count: 8,469 
• Modeled Residue Count: 992 
• Deposited Residue Count: 1,018 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase B	A, B	509	Serratia marcescens	Mutation(s): 0  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
FO0 (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth B]	6-azanyl-11-methyl-2-oxidanylidene-N-[(1S)-1-pyridin-3-ylethyl]-1,7,9-triazatricyclo[8.4.0.0^{3,8}]tetradeca-3,5,7,9,11,13-hexaene-5-carboxamide C20 H18 N6 O2 FHRKZGQIKPGLAU-LBPRGKRZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.846	α = 90
b = 104.077	β = 90
c = 186.286	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: 2021-06-16 
Deposition Author(s): Jiang, X., Yuan, P.T.

Revision History  

• Version 1.0: 2021-06-16
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary