Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100471.07 
• Atom Count: 6859 
• Residue Count: 842 
• Unique protein chains: 1

1RS6

Rat neuronal NOS heme domain with D-lysine-D-nitroarginine amide bound

• DOI: 10.2210/pdb1RS6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2003-12-09 Released: 2004-05-18 
• Deposition Author(s): Flinspach, M., Li, H., Jamal, J., Yang, W., Huang, H., Silverman, R.B., Poulos, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.254 
• R-Value Work: 0.221 

Literature

Structures of the Neuronal and Endothelial Nitric Oxide Synthase Heme Domain with d-Nitroarginine-Containing Dipeptide Inhibitors Bound.

Flinspach, M., Li, H., Jamal, J., Yang, W., Huang, H., Silverman, R.B., Poulos, T.L.

(2004) Biochemistry 43: 5181-5187

• PubMed: 15122883 
• DOI: 10.1021/bi0361867
• Primary Citation of Related Structures:  
  1RS9, 1RS8, 1RS7


• PubMed Abstract: 
  

In a continuing effort to unravel the structural basis for isoform-selective inhibition of nitric oxide synthase (NOS) by various inhibitors, we have determined the crystal structures of the nNOS and eNOS heme domain bound with two D-nitroarginine-containing dipeptide inhibitors, D-Lys-D-Arg(NO)2-NH(2) and D-Phe-D-Arg(NO)2-NH(2). These two dipeptide inhibitors exhibit similar binding modes in the two constitutive NOS isozymes, which is consistent with the similar binding affinities for the two isoforms as determined by K(i) measurements. The D-nitroarginine-containing dipeptide inhibitors are not distinguished by the amino acid difference between nNOS and eNOS (Asp 597 and Asn 368, respectively) which is key in controlling isoform selection for nNOS over eNOS observed for the L-nitroarginine-containing dipeptide inhibitors reported previously [Flinspach, M., et al. (2004) Nat. Struct. Mol. Biol. 11, 54-59]. The lack of a free alpha-amino group on the D-nitroarginine moiety makes the dipeptide inhibitor steer away from the amino acid binding pocket near the active site. This allows the inhibitor to extend into the solvent-accessible channel farther away from the active site, which enables the inhibitors to explore new isoform-specific enzyme-inhibitor interactions. This might be the structural basis for why these D-nitroarginine-containing inhibitors are selective for nNOS (or eNOS) over iNOS.

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Related Citations: 

• The novel binding mode of N-alkyl-N'-hydroxyguanidine to neuronal nitric oxide synthase provides mechanistic insights into NO biosynthesis
  Li, H.,Shimizu, H.,Flinspach, M.L.,Jamal, J.,Yang, W.,Xian, M.,Cai, T.,Wen, E.Z.,Jia, Q.,Wang, P.G.,Poulos, T.L.
  (2002) Biochemistry 41: 13868




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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Nitric-oxide synthase, brain	A, B	421	Rattus norvegicus	Mutation(s): 0  Gene Names: Nos1 (Bnos) EC: 1.14.13.39
Find proteins for P29476 (Rattus norvegicus) Go to UniProtKB:  P29476

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	A, B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MTL	A, B	D-MANNITOL C6 H14 O6 FBPFZTCFMRRESA-KVTDHHQDSA-N
HEM	A, B	PROTOPORPHYRIN IX CONTAINING FE HEME C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
H4B	A, B	5,6,7,8-TETRAHYDROBIOPTERIN C9 H15 N5 O3 FNKQXYHWGSIFBK-RPDRRWSUSA-N
DP2	A, B	L-LYSYL-N~5~-[(Z)-(2,2-DIHYDROXYHYDRAZINO)(IMINO)METHYL]-L-ORNITHINAMIDE D-LYSINE-D-NITROARGININE AMIDE C12 H28 N8 O4 VKBOUZQMRKGFCB-RKDXNWHRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.254 
• R-Value Work: 0.221 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.590	α = 90.00
b = 109.810	β = 90.00
c = 164.670	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	phasing
DENZO	data reduction
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-12-09 
• Released Date: 2004-05-18 
• Deposition Author(s): Flinspach, M., Li, H., Jamal, J., Yang, W., Huang, H., Silverman, R.B., Poulos, T.L.

Revision History 

• Version 1.0: 2004-05-18
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-09-21
  Type: Non-polymer description