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 4UWN | pdb_00004uwn

Lysozyme soaked with a ruthenium based CORM with a methione oxide ligand (complex 6b)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.166 (Depositor) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4UWN

This is version 1.5 of the entry. See complete history. 

Literature

A Contribution to the Rational Design of Ru(Co)3Cl2L Complexes for in Vivo Delivery of Co.

Seixas, J.D., Santos, M.F.A., Mukhopadhyay, A., Coelho, A.C., Reis, P.M., Veiros, L.F., Marques, A.R., Penacho, N., Goncalves, A.M.L., Romao, M.J., Bernardes, G.J.L., Santos-Silva, T., Romao, C.C.

(2015) Dalton Trans 44: 5058

  • DOI: https://doi.org/10.1039/c4dt02966f
  • Primary Citation Related Structures: 
    4UWN, 4UWU, 4UWV

  • PubMed Abstract: 

    A few ruthenium based metal carbonyl complexes, e.g. CORM-2 and CORM-3, have therapeutic activity attributed to their ability to deliver CO to biological targets. In this work, a series of related complexes with the formula [Ru(CO)3Cl2L] (L = DMSO (3), L-H3CSO(CH2)2CH(NH2)CO2H) (6a); D,L-H3CSO(CH2)2CH(NH2)CO2H (6b); 3-NC5H4(CH2)2SO3Na (7); 4-NC5H4(CH2)2SO3Na (8); PTA (9); DAPTA (10); H3CS(CH2)2CH(OH)CO2H (11); CNCMe2CO2Me (12); CNCMeEtCO2Me (13); CN(c-C3H4)CO2Et) (14)) were designed, synthesized and studied. The effects of L on their stability, CO release profile, cytotoxicity and anti-inflammatory properties are described. The stability in aqueous solution depends on the nature of L as shown using HPLC and LC-MS studies. The isocyanide derivatives are the least stable complexes, and the S-bound methionine oxide derivative is the more stable one. The complexes do not release CO gas to the headspace, but release CO2 instead. X-ray diffraction of crystals of the model protein Hen Egg White Lysozyme soaked with 6b (4UWN) and 8 (4UWN) shows the addition of Ru(II)(CO)(H2O)4 at the His15 binding site. Soakings with 7(4UWN) produced the metallacarboxylate [Ru(COOH)(CO)(H2O)3](+) bound to the His15 site. The aqueous chemistry of these complexes is governed by the water-gas shift reaction initiated with the nucleophilic attack of HO(-) on coordinated CO. DFT calculations show this addition to be essentially barrierless. The complexes have low cytotoxicity and low hemolytic indices. Following i.v. administration of CORM-3, the in vivo bio-distribution of CO differs from that obtained with CO inhalation or with heme oxygenase stimulation. A mechanism for CO transport and delivery from these complexes is proposed.


  • Organizational Affiliation: 
    • Instituto de Tecnologia Química e Biológica-António Xavier da Universidade Nova de Lisboa, Av. da República, EAN, 2780-157 Oeiras, Portugal. ccr@itqb.unl.pt.

Macromolecule Content 

  • Total Structure Weight: 15.07 kDa 
  • Atom Count: 1,173 
  • Modeled Residue Count: 129 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LYSOZYME C129Gallus gallusMutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00698
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RU

Query on RU



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A]
RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
B [auth A],
L [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
CMO

Query on CMO



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.212 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.166 (Depositor) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.93α = 90
b = 79.93β = 90
c = 36.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Advisory, Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary