8PFT | pdb_00008pft

X-ray structure of the adduct formed upon reaction of Lysozyme with K2[Ru2(D-p-FPhF)(CO3)3] in condition A

• PDB DOI: https://doi.org/10.2210/pdb8PFT/pdb

• Classification: PROTEIN BINDING
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2023-06-16 Released: 2023-07-19 
• Deposition Author(s): Teran, A., Ferraro, G., Merlino, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.246 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.212 (DCC) 

Starting Model: experimental

Literature

Charge effect in protein metalation reactions by diruthenium complexes

Herrero Dominguez, S., Teran, A., Ferraro, G., Sanchez-Pelaez, A.E., Merlino, A.

(2023) Inorg Chem Front 

• DOI: https://doi.org/10.1039/D3QI01192E

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 15.51 kDa 
• Atom Count: 1,204 
• 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
YJT (Subject of Investigation/LOI)	D [auth A], E [auth A]	6,8-bis(4-fluorophenyl)-1,5-bis(oxidanyl)-2,4-dioxa-6,8-diaza-1$l^{4},5$l^{4}-diruthenabicyclo[3.3.0]octan-3-one C14 H12 F2 N2 O5 Ru2 MTQUSIMNYQTHAA-UHFFFAOYSA-J
NO3	F [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.246 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.212 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.75	α = 90
b = 77.75	β = 90
c = 37.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Teran, A., Ferraro, G., Merlino, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary