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:

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 Gene Names: CYCS, CYC
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
Protein Feature View 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		Ligand Interaction
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		Ligand Interaction
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		Ligand Interaction
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		Ligand Interaction

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