5E9R | pdb_00005e9r

X-ray structure of the complex between lysozyme and the compound fac, cis-[RuII(CO)3Cl2(N3-MBI), MBI=N-methyl-benzimidazole

• PDB DOI: https://doi.org/10.2210/pdb5E9R/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2015-10-15 Released: 2016-10-26 
• Deposition Author(s): Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Literature

{Ru(CO)x}-core Complexes with N-Methylbenzimidazole (MBI) and 5,6-Dimethylbenzimidazole (DMBI) as Possible Metal Based Drugs and CO Release Materials. Synthesis, X-ray Structure and Evaluation of Cytotoxic Activity against Human Cancer Cells

Merlino, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.72 kDa 
• Atom Count: 1,189 
• 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  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
5LN	B [auth A]	chloranyl-bis(hydroxymethyl)-bis(oxidanyl)ruthenium C2 H8 Cl O4 Ru KMSYBSCWEKUGEO-UHFFFAOYSA-K
CL	E [auth A], F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO	C [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.5	α = 90
b = 78.5	β = 90
c = 36.309	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Merlino, A.

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary