Download MendeleyCharge 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
8PFV
X-ray structure of the adduct formed upon reaction of Lysozyme with [Ru2Cl(DAniF)(O2CCH3)3] in condition A
- PDB DOI: https://doi.org/10.2210/pdb8PFV/pdb
- Classification: PROTEIN BINDING
- Organism(s): Gallus gallus
- Mutation(s): No
- Deposited: 2023-06-16 Released: 2023-07-19
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.46 Å
- R-Value Free: 0.211
- R-Value Work: 0.179
This is version 2.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Lysozyme C | A [auth AAA] | 129 | Gallus gallus | Mutation(s): 0 EC: 3.2.1.17 |  |
UniProt | |||||
Find proteins for P00698 (Gallus gallus) Explore P00698 Go to UniProtKB: P00698 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00698 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| YMQ (Subject of Investigation/LOI) Query on YMQ | I [auth AAA] | 9,11-bis(4-methoxyphenyl)-3,7-dimethyl-2,4,6,8-tetraoxa-9,11-diaza-1$l^{4},5$l^{4}-diruthenatricyclo[3.3.3.0^{1,5}]undecane C19 H24 N2 O6 Ru2 ILDPKHMKTATIQB-UHFFFAOYSA-N |  | ||
| NO3 Query on NO3 | D [auth AAA], E [auth AAA], F [auth AAA], G [auth AAA], H [auth AAA] | NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N |  | ||
| CL Query on CL | B [auth AAA] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | C [auth AAA] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.46 Å
- R-Value Free: 0.211
- R-Value Work: 0.179
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 78.35 | α = 90 |
| b = 78.35 | β = 90 |
| c = 37.64 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| autoPROC | data reduction |
| autoPROC | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2023-07-19 Deposition Author(s): Teran, A., Ferraro, G., Merlino, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2023-07-19
Type: Initial release - Version 2.0: 2023-10-18
Type: Coordinate replacement
Reason: Ligand identity
Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
