2NSR | pdb_00002nsr

Nitromethane Modified Horse Heart Myoglobin

PDB DOI: https://doi.org/10.2210/pdb2NSR/pdb

Classification: OXYGEN STORAGE/TRANSPORT
Organism(s): Equus caballus
Mutation(s): No

Deposited: 2006-11-06 Released: 2007-11-06
Deposition Author(s): Copeland, D.M., West, A.H., Richter-Addo, G.B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.231 (Depositor), 0.133 (DCC)
R-Value Work:
0.160 (Depositor)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Nitrosoalkane and Nitrosoarene Binding to Myoglobin and Heme Models

Copeland, D.M., West, A.H., Richter-Addo, G.B.

To be published.

Macromolecule Content

Total Structure Weight: 17.84 kDa
Atom Count: 1,384
Modeled Residue Count: 152
Deposited Residue Count: 153
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myoglobin	A	153	Equus caballus	Mutation(s): 0 EC: 1.11.1 (UniProt), 1.7 (UniProt)
UniProt
Find proteins for P68082 (Equus caballus) Explore P68082 Go to UniProtKB: P68082
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68082
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NSM Query on NSM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	NITROSOMETHANE C H₃ N O IMHRONYAKYWGCC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.231 (Depositor), 0.133 (DCC)
R-Value Work: 0.160 (Depositor)
R-Value Observed: 0.163 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.344	α = 90
b = 28.74	β = 106
c = 63.471	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-11-06

Deposition Author(s):

Copeland, D.M.

West, A.H.

Richter-Addo, G.B.

Revision History (Full details and data files)

Version 1.0: 2007-11-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

2NSR | pdb_00002nsr

Nitromethane Modified Horse Heart Myoglobin

Literature

Nitrosoalkane and Nitrosoarene Binding to Myoglobin and Heme Models

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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