1EQD

CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH CN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Nitric oxide binding to nitrophorin 4 induces complete distal pocket burial.

Weichsel, A.Andersen, J.F.Roberts, S.A.Montfort, W.R.

(2000) Nat.Struct.Mol.Biol. 7: 551-554

  • DOI: 10.1038/76769
  • Primary Citation of Related Structures:  1D3S, 1ERX

  • PubMed Abstract: 
  • The nitrophorins comprise an unusual family of proteins that use ferric (Fe(III)) heme to transport highly reactive nitric oxide (NO) from the salivary gland of a blood sucking bug to the victim, resulting in vasodilation and reduced blood coagulatio ...

    The nitrophorins comprise an unusual family of proteins that use ferric (Fe(III)) heme to transport highly reactive nitric oxide (NO) from the salivary gland of a blood sucking bug to the victim, resulting in vasodilation and reduced blood coagulation. We have determined structures of nitrophorin 4 in complexes with H2O, cyanide and nitric oxide. These structures reveal a remarkable feature: the nitrophorins have a broadly open distal pocket in the absence of NO, but upon NO binding, three or more water molecules are expelled and two loops fold into the distal pocket, resulting in the packing of hydrophobic groups around the NO molecule and increased distortion of the heme. In this way, the protein apparently forms a 'hydrophobic trap' for the NO molecule. The structures are very accurate, ranging between 1.6 and 1.4 A resolutions.


    Related Citations: 
    • Crystal structure of a nitric oxide transport protein from a blood-sucking insect.
      Weichsel, A.,Andresen, J.F.,Champagne, D.E.,Walker, F.A.,Montfort, W.R.
      (1998) Nat.Struct.Mol.Biol. 5: 304
    • The crystal structure of nitrophorin 4 at 1.5 A resolution: transport of nitric oxide by a lipocalin-based heme protein.
      Andersen, J.F.,Weichsel, A.,Balfour, C.A.,Champagne, D.E.,Montfort, W.R.
      (1998) Structure 6: 1315


    Organizational Affiliation

    Department of Biochemistry, University of Arizona, Tucson, Arizona 85721, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITROPHORIN 4
A
184Rhodnius prolixusEC: 1.7.6.1
Find proteins for Q94734 (Rhodnius prolixus)
Go to UniProtKB:  Q94734
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEV
Query on HEV

Download SDF File 
Download CCD File 
A
5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC ACID FERROUS COMPLEX
1,3-DEDIMETHYL-1,3-DIVINYL HEME
C36 H32 Fe N4 O4
KPGBVOKZHGYTDW-RFPWDTAWDE
 Ligand Interaction
CYN
Query on CYN

Download SDF File 
Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.036α = 90.00
b = 42.652β = 94.18
c = 52.559γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MADNESSdata reduction
CCP4data scaling
X-PLORmodel building
SHELXL-97refinement
MADNESSdata collection
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Database references