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: 100.15 kDa 
• Atom Count: 7441 
• Modelled Residue Count: 817 
• Deposited Residue Count: 840 
• Unique protein chains: 1

1ZZQ

Rat nNOS D597N mutant with L-N(omega)-Nitroarginine-(4R)-amino-L-proline amide bound

• PDB DOI: 10.2210/pdb1ZZQ/pdb

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


• Deposited: 2005-06-14 Released: 2005-12-06 
• Deposition Author(s): Li, H., Flinspach, M.L., Igarashi, J., Jamal, J., Yang, W., Gomez-Vidal, J.A., Litzinger, E.A., Silverman, R.B., Poulos, T.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

Exploring the Binding Conformations of Bulkier Dipeptide Amide Inhibitors in Constitutive Nitric Oxide Synthases.

Li, H., Flinspach, M.L., Igarashi, J., Jamal, J., Yang, W., Litzinger, E.A., Huang, H., Erdal, E.P., Silverman, R.B., Poulos, T.L.

(2005) Biochemistry 44: 15222-15229

• PubMed: 16285725 
• DOI: 10.1021/bi0513610
• Primary Citation of Related Structures:  
  1ZZQ, 1ZZR, 1ZZS, 1ZZT, 1ZZU


• PubMed Abstract: 
  

A series of L-nitroarginine-based dipeptide inhibitors are highly selective for neuronal nitric oxide synthase (nNOS) over the endothelial isoform (eNOS). Crystal structures of these dipeptides bound to both isoforms revealed two different conformations, curled in nNOS and extended in eNOS, corresponding to higher and lower binding affinity to the two isoforms, respectively. In previous studies we found that the primary reason for selectivity is that Asp597 in nNOS, which is Asn368 in eNOS, provides greater electrostatic stabilization in the inhibitor complex. While this is the case for smaller dipeptide inhibitors, electrostatic stabilization may no longer be the sole determinant for isoform selectivity with bulkier dipeptide inhibitors. Another residue farther away from the active site, Met336 in nNOS (Val106 in eNOS), is in contact with bulkier dipeptide inhibitors. Double mutants were made to exchange the D597/M336 pair in nNOS with N368/V106 in eNOS. Here we report crystal structures and inhibition constants for bulkier dipeptide inhibitors bound to nNOS and eNOS that illustrate the important role played by residues near the entry to the active site in isoform selective inhibition.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Molecular Biology and Biochemistry, 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	420	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
DP9	H [auth A], M [auth B]	L-N(OMEGA)-NITROARGININE-(4R)-AMINO-L-PROLINE AMIDE C11 H22 N8 O4 IUFRDGFKAVLPFZ-CSMHCCOUSA-N
H4B	G [auth A], L [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C9 H15 N5 O3 FNKQXYHWGSIFBK-RPDRRWSUSA-N
MTL	E [auth A], J [auth B]	D-MANNITOL C6 H14 O6 FBPFZTCFMRRESA-KVTDHHQDSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	C [auth A], I [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
DP9	BindingDB:  1ZZQ	Ki: 100 (nM) from 1 assay(s)
		IC50: 640 (nM) from 1 assay(s)
	Binding MOAD:  1ZZQ	Ki: 2.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.244 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.86	α = 90
b = 110.32	β = 90
c = 164.6	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: 2005-06-14 
• Released Date: 2005-12-06 
Deposition Author(s): Li, H., Flinspach, M.L., Igarashi, J., Jamal, J., Yang, W., Gomez-Vidal, J.A., Litzinger, E.A., Silverman, R.B., Poulos, T.L.

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations