6K5Q | pdb_00006k5q

Crystal structure of lysozyme complexed with a bioactive compound from Jatropha gossypiifolia

• PDB DOI: https://doi.org/10.2210/pdb6K5Q/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-30 Released: 2020-05-27 
• Deposition Author(s): Kanal Elamparithi, B., Ankur, T., Sivakumar, M., Gunasekaran, K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of lysozyme complexed with a bioactive compound from Jatropha gossypiifolia

Kanal Elamparithi, B., Ankur, T., Sivakumar, M., Gunasekaran, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 14.98 kDa 
• Atom Count: 1,174 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysozyme C	A	129	Gallus gallus	Mutation(s): 0  Gene Names: LYZ EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D2L (Subject of Investigation/LOI)	E [auth A]	[(3R,6R)-6-methyloctan-3-yl] 2-[(2S,4S,6R)-2-[(2S)-2-ethylpentyl]-6-methyl-1-(2-oxidanylideneethyl)piperidin-4-yl]ethanesulfonate C26 H51 N O4 S KIJFPQMAPUEGBO-GBYFVPISSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.18 Å
• R-Value Free:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.074	α = 90
b = 77.074	β = 90
c = 38.654	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Kanal Elamparithi, B., Ankur, T., Sivakumar, M., Gunasekaran, K.

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary