1PM1

Crystal structure of nitrophorin 2 L122V/L132V mutant complex with imidazole

PDB DOI: https://doi.org/10.2210/pdb1PM1/pdb

Classification: BLOOD CLOTTING INHIBITOR
Organism(s): Rhodnius prolixus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2003-06-09 Released: 2004-06-22
Deposition Author(s): Weichsel, A., Montfort, W.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.177
R-Value Work: 0.154
R-Value Observed: 0.155

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

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

Weichsel, A., Montfort, W.R.

To be published.

Macromolecule Content

Total Structure Weight: 20.74 kDa
Atom Count: 1,711
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 [auth X]	180	Rhodnius prolixus	Mutation(s): 2
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 X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.177
R-Value Work: 0.154
R-Value Observed: 0.155
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.31	α = 90
b = 125.47	β = 90
c = 33.88	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
d*TREK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2004-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-06-22
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: 2021-10-27
Changes: Database references, Derived calculations
Version 1.4: 2023-08-16
Changes: Data collection, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.