1PEE

Crystal Structure of Nitrophorin 2 complex with imidazole

PDB DOI: https://doi.org/10.2210/pdb1PEE/pdb

Classification: SIGNALING PROTEIN
Organism(s): Rhodnius prolixus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2003-05-21 Released: 2004-06-01
Deposition Author(s): Weihsel, A., Montfort, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.240
R-Value Work: 0.186
R-Value Observed: 0.188

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Conformational change and heme ruffling in nitrophorin 2, a nitric oxide carrier from kissing bug.

Weihsel, A., Montfort, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 20.77 kDa
Atom Count: 1,629
Modelled Residue Count: 180
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin 2	A	180	Rhodnius prolixus	Mutation(s): 0
UniProt
Find proteins for Q26241 (Rhodnius prolixus) Explore Q26241 Go to UniProtKB: Q26241
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q26241
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] mmCIF 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]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 ?
R-Value Free: 0.240
R-Value Work: 0.186
R-Value Observed: 0.188
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 34.68	α = 90
b = 34.68	β = 90
c = 258.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
d*TREK	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-06-01

Deposition Author(s):

Weihsel, A.

Montfort, W.R.

Revision History (Full details and data files)

Version 1.0: 2004-06-01
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary

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Help and Resources

1PEE

Crystal Structure of Nitrophorin 2 complex with imidazole

Conformational change and heme ruffling in nitrophorin 2, a nitric oxide carrier from kissing bug.

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)