8PFX | pdb_00008pfx

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

PDB DOI: https://doi.org/10.2210/pdb8PFX/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.214 (Depositor), 0.220 (DCC)
R-Value Work:
0.192 (Depositor), 0.201 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 16.27 kDa
Atom Count: 1,254
Modeled Residue Count: 129
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00698
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YJT (Subject of Investigation/LOI) Query on YJT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	F [auth A], G [auth A], H [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		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]