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
View more details

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

Find similar proteins by:

(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]
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]

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

View Full Validation Report

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.