4NXC

SPERM WHALE MYOGLOBIN UNDER 30 BAR NITROUS Oxide

PDB DOI: https://doi.org/10.2210/pdb4NXC/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Physeter catodon
Mutation(s): No

Deposited: 2013-12-09 Released: 2014-09-24
Deposition Author(s): Colloc'h, N., Prange, T., Vallone, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.225
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystallographic Studies with Xenon and Nitrous Oxide Provide Evidence for Protein-dependent Processes in the Mechanisms of General Anesthesia

Abraini, J.H., Marassio, G., David, H.N., Vallone, B., Prange, T., Colloc'h, N.

(2014) Anesthesiology 121: 1018-1027

PubMed: 25211169 Search on PubMed
DOI: https://doi.org/10.1097/ALN.0000000000000435
Primary Citation of Related Structures:
4NWE, 4NWH, 4NXA, 4NXC, 4O4T, 4O4Z

PubMed Abstract:
The mechanisms by which general anesthetics, including xenon and nitrous oxide, act are only beginning to be discovered. However, structural approaches revealed weak but specific protein-gas interactions.

Organizational Affiliation

From the Faculté de Médecine, Université de Caen Basse Normandie, Normandie-Université, Caen, France (J.H.A., G.M.); Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France (J.H.A.); Département d'Anesthésiologie, Université Laval, Quebec City, Québec, Canada (J.H.A., H.N.D.); Centre de Recherche Hôtel-Dieu de Lévis, CSSS Alphonse-Desjardins, Lévis, Québec, Canada (H.N.D.); Department of Biochemical Sciences, University of Rome La Sapienza, Rome, Italy (B.V.); LCRB UMR 8015, Université Paris Descartes-CNRS, Faculté de Pharmacie, Paris, France (T.P.); ISTCT UMR 6301, CNRS, CERVOxy group, GIP Cyceron, Caen, France (N.C.); ISTCT UMR 6301, Université de Caen Basse Normandie, Normandie-Université, Caen, France (N.C.); and ISTCT UMR 6301, CEA DSV/I2BM, Caen, France (N.C.).

Macromolecule Content

Total Structure Weight: 18.58 kDa
Atom Count: 1,355
Modelled Residue Count: 153
Deposited Residue Count: 154
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	154	Physeter catodon	Mutation(s): 0
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185 Go to UniProtKB: P02185
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A]	E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
N2O Query on N2O Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	H [auth A], I [auth A], J [auth A], K [auth A]	NITROUS OXIDE N₂ O GQPLMRYTRLFLPF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.225
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.449	α = 90
b = 30.545	β = 104.57
c = 63.634	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-09-24

Deposition Author(s):

Colloc'h, N.

Prange, T.

Vallone, B.

Revision History (Full details and data files)

Version 1.0: 2014-09-24
Type: Initial release
Version 1.1: 2014-12-17
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description