5NCV

Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene

PDB DOI: https://doi.org/10.2210/pdb5NCV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-03-06 Released: 2018-03-14
Deposition Author(s): Alex, J.M., Rennie, M.L., Crowley, P.B.
Funding Organization(s): Science Funding Ireland

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.201
R-Value Work: 0.170
R-Value Observed: 0.172

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Phosphonated Calixarene as a ""Molecular Glue"" for Protein Crystallization

Alex, J.M., Rennie, M.L., Volpi, S., Sansone, F., Casnati, A., Crowley, P.B.

(2018) Cryst Growth Des 18: 2467-2473

DOI: https://doi.org/10.1021/acs.cgd.8b00092

Macromolecule Content

Total Structure Weight: 27.76 kDa
Atom Count: 2,303
Modelled Residue Count: 208
Deposited Residue Count: 216
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 iso-1	A, B	108	Saccharomyces cerevisiae S288C	Mutation(s): 1 Gene Names: CYC1, YJR048W, J1653
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044 Go to UniProtKB: P00044
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8TE Query on 8TE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	D [auth A], E [auth A], H [auth B]	p-Methylphosphonatocalix[4]arene C₃₂ H₃₆ O₁₆ P₄ HXGDFDVLRPRMJW-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.201
R-Value Work: 0.170
R-Value Observed: 0.172
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 28.917	α = 90
b = 80.227	β = 93.07
c = 47.807	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Alex, J.M.

Rennie, M.L.

Crowley, P.B.

Funding Organization	Location	Grant Number
Science Funding Ireland	Ireland	13/CDA/2168

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2018-03-28
Changes: Data collection, Database references
Version 1.2: 2018-11-14
Changes: Data collection, Database references
Version 1.3: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary

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5NCV

Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene

Phosphonated Calixarene as a ""Molecular Glue"" for Protein Crystallization

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)