Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 100.41 kDa 
• Atom Count: 7451 
• Modelled Residue Count: 817 
• Deposited Residue Count: 842 
• Unique protein chains: 1

1P6K

Rat neuronal NOS D597N mutant heme domain with L-N(omega)-nitroarginine-2,4-L-diaminobutyric amide bound

• PDB DOI: 10.2210/pdb1P6K/pdb

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


• Deposited: 2003-04-29 Released: 2004-01-13 
• Deposition Author(s): 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.250 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 

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

• PubMed: 14718923 
• DOI: 10.1038/nsmb704
• Primary Citation of 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.

---

Related Citations: 

• CRYSTAL STRUCTURE OF CONSTITUTIVE ENDOTHELIAL NITRIC OXIDE SYNTHASE: A PARADIGM FOR PTERIN FUNCTION INVOLVING A NOVEL METAL CENTER
  Raman, C.S., Li, H., Martasek, P., Kral, V., Masters, B.S.S., Poulos, T.L.
  (1998) Cell 95: 939

• 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., Jamal, J., Yang, W., Xian, M., Cai, T., Wen, E.Z., Jia, Q., Wang, P.G., Poulos, T.L.
  (2002) Biochemistry 41: 13868

---

Organizational Affiliation: 

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

Macromolecules

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	F [auth A], K [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DP1	H [auth A], M [auth B]	L-N(OMEGA)-NITROARGININE-2,4-L-DIAMINOBUTYRIC AMIDE C10 H22 N8 O4 KUZKVXUOMSVPOA-BQBZGAKWSA-N
H4B	G [auth A], L [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C9 H15 N5 O3 FNKQXYHWGSIFBK-RPDRRWSUSA-N
MTL	C [auth A], I [auth B]	D-MANNITOL C6 H14 O6 FBPFZTCFMRRESA-KVTDHHQDSA-N
ZN	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A], J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
DP1	Binding MOAD:  1P6K	Ki: 6.70e+4 (nM) from 1 assay(s)
	BindingDB:  1P6K	Ki: 130 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.250 
• R-Value Work: 0.225 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.77	α = 90
b = 109.74	β = 90
c = 164.39	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-29 
• Released Date: 2004-01-13 
Deposition Author(s): 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.

Revision History  

• 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: 2021-10-27
  Changes: Database references, Derived calculations