1Q2O | pdb_00001q2o

Bovine endothelial nitric oxide synthase N368D mutant heme domain dimer with L-N(omega)-nitroarginine-2,4-L-diaminobutyramide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.220 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1Q2O

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural basis for dipeptide amide isoform-selective inhibition of neuronal nitric oxide synthase.

Flinspach, M.L.Li, H.Jamal, J.Yang, W.Huang, H.Hah, J.M.Gomez-Vidal, J.A.Litzinger, E.A.Silverman, R.B.Poulos, T.L.

(2004) Nat Struct Mol Biol 11: 54-59

  • DOI: https://doi.org/10.1038/nsmb704
  • Primary Citation Related Structures: 
    1P6H, 1P6I, 1P6J, 1P6K, 1P6L, 1P6M, 1P6N, 1Q2O

  • PubMed Abstract: 

    Three nitric oxide synthase (NOS) isoforms, eNOS, nNOS and iNOS, generate nitric oxide (NO) crucial to the cardiovascular, nervous and host defense systems, respectively. Development of isoform-selective NOS inhibitors is of considerable therapeutic importance. Crystal structures of nNOS-selective dipeptide inhibitors in complex with both nNOS and eNOS were solved and the inhibitors were found to adopt a curled conformation in nNOS but an extended conformation in eNOS. We hypothesized that a single-residue difference in the active site, Asp597 (nNOS) versus Asn368 (eNOS), is responsible for the favored binding in nNOS. In the D597N nNOS mutant crystal structure, a bound inhibitor switches to the extended conformation and its inhibition of nNOS decreases >200-fold. Therefore, a single-residue difference is responsible for more than two orders of magnitude selectivity in inhibition of nNOS over eNOS by L-N(omega)-nitroarginine-containing dipeptide inhibitors.


  • Organizational Affiliation
    • Department of Molecular Biology and Biochemistry and the Program in Macromolecular Structure, University of California, Irvine, California 92697-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 96.7 kDa 
  • Atom Count: 7,278 
  • Modeled Residue Count: 810 
  • Deposited Residue Count: 832 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitric-oxide synthase, endothelial
A, B
416Bos taurusMutation(s): 1 
Gene Names: NOS3
EC: 1.14.13.39
UniProt
Find proteins for P29473 (Bos taurus)
Explore P29473 
Go to UniProtKB:  P29473
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29473
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DP1

Query on DP1



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B]
L-N(OMEGA)-NITROARGININE-2,4-L-DIAMINOBUTYRIC AMIDE
C10 H22 N8 O4
KUZKVXUOMSVPOA-BQBZGAKWSA-N
H4B

Query on H4B



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
CAC

Query on CAC



Download:Ideal Coordinates CCD File
C [auth A],
J [auth B]
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth A],
O [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.220 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.908α = 90
b = 106.989β = 90
c = 156.989γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection
  • Version 1.5: 2024-04-03
    Changes: Refinement description