4RSZ

The X-ray structure of the Primary Adduct formed in the Reaction between Cisplatin and Cytochrome c

PDB DOI: https://doi.org/10.2210/pdb4RSZ/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Equus caballus
Mutation(s): No

Deposited: 2014-11-12 Released: 2015-01-14
Deposition Author(s): Merlino, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.282
R-Value Work: 0.231
R-Value Observed: 0.234

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

The X-ray structure of the primary adducts formed in the reaction between cisplatin and cytochrome c.

Ferraro, G., Messori, L., Merlino, A.

(2015) Chem Commun (Camb) 51: 2559-2561

PubMed: 25567806 Search on PubMed
DOI: https://doi.org/10.1039/c4cc09056j
Primary Citation of Related Structures:
4RSZ

PubMed Abstract:
In the present study, the interactions between cisplatin and cytochrome c are investigated. Based on high-resolution X-ray diffraction data, two monometalated species, i.e. cyt c-Pt(NH3)2 and cyt c-Pt(NH3)2Cl, are found to be the main adducts that form in the reaction between the protein and the drug. Both monodentate and bidentate platinum coordination to the protein is observed, with platinum binding either to Met65 or to Met65 and Glu61, simultaneously.

Organizational Affiliation

Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, I-80126, Napoli, Italy. antonello.merlino@unina.it.

Macromolecule Content

Total Structure Weight: 76.75 kDa
Atom Count: 5,421
Modelled Residue Count: 624
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	A, B, C, D, E A, B, C, D, E, F	104	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P00004 (Equus caballus) Explore P00004 Go to UniProtKB: P00004
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00004
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain EA [auth F] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E]	EA [auth F] G [auth A] K [auth B] Q [auth C] V [auth D] EA [auth F], G [auth A], K [auth B], Q [auth C], V [auth D], Z [auth E]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain EA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Z [auth E]
CPT Query on CPT Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain GA [auth F] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain W [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain W [auth D]	AA [auth E], GA [auth F], H [auth A], M [auth B], W [auth D]	Cisplatin Cl₂ H₆ N₂ Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain W [auth D] Interactions & Density Focus chain AA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain W [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain L [auth B] MOL2 format, chain FA [auth F] MOL2 format, chain L [auth B]	FA [auth F], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FA [auth F] Focus chain L [auth B] Interactions & Density Focus chain FA [auth F] Focus chain L [auth B]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain DA [auth E] SDF format, chain HA [auth F] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D]	BA [auth E] CA [auth E] DA [auth E] HA [auth F] I [auth A] BA [auth E], CA [auth E], DA [auth E], HA [auth F], I [auth A], IA [auth F], J [auth A], N [auth B], O [auth B], P [auth B], R [auth C], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.282
R-Value Work: 0.231
R-Value Observed: 0.234
Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.344	α = 90
b = 120.344	β = 90
c = 36.673	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Merlino, A.

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 1.1: 2015-02-25
Changes: Database references
Version 2.0: 2021-03-10
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description