1P6H | pdb_00001p6h

Rat neuronal NOS heme domain with L-N(omega)-nitroarginine-2,4-L-diaminobutyric amide bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.273 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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: 100.05 kDa 
  • Atom Count: 7,314 
  • Modeled Residue Count: 817 
  • Deposited Residue Count: 842 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitric-oxide synthase, brain
A, B
421Rattus norvegicusMutation(s): 0 
EC: 1.14.13.39
UniProt
Find proteins for P29476 (Rattus norvegicus)
Explore P29476 
Go to UniProtKB:  P29476
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29476
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



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

Query on DP1



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

Query on ZN



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

Query on ACT



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free:  0.273 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.223 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.94α = 90
b = 110.22β = 90
c = 164.77γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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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: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations