BIOMD0000000198
type: SBMLModel
species: 481231
parameter: metaid_0000038
is version of: GO:0007263
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
rule: 481413
is described by: http://identifiers.org/pubmed/8573563
occurs in: http://identifiers.org/taxonomy/9913
parameter: metaid_0000045
area units: metaid_0000005
time units: metaid_0000041
species: 481211
parameter: metaid_0300046
is version of: GO:0031282
creator:
  ORG:
    orgname: Department of Biological Chemistry, University of Michigan, Michigan
  n:
    given: James R
    family: Stone
units def: metaid_0000031
modified:
  W3 CDTF: Wed May 16 11:00:59 BST 2012
units def: metaid_0000035
species: 481351
parameter: metaid_0000036
parameter: metaid_0000042
reaction: metaid_0000052
species: 481191
parameter: metaid_0500046
parameter: metaid_0000041
species: 481271
parameter: metaid_0000044
parameter: metaid_0000037
reaction: metaid_0000053
is: MODEL4779732381
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
species: 482411
creator:
  ORG:
    orgname: Department of Biological Chemistry, University of Michigan, Michigan
  n:
    given: Michael A
    family: Marletta
species: 481171
parameter: metaid_0000040
rule: 581413
parameter: metaid_0000043
species: 481391
reaction: metaid_0000051
reaction: metaid_0000049
units def: metaid_0010031
units def: metaid_0020031
name: Stone1996_NOsGC
rule: 481412
species: 481331
substance units: metaid_0000030
compartment: 481131
species: 481411
created:
  W3 CDTF: Tue Oct 21 16:19:25 BST 2008
reaction: metaid_0000050
units def: metaid_0000030
notes: This features the two step binding of NO to soluble Guanylyl Cyclase as proposed byStone JR, Marletta MA. Biochemistry (1996) 35(4):1093-9 . There is a fast step binding scheme and a slow step binding scheme. The difference lies in the binding of a NO to a non-heme site on sGC, which may not necessarily be the same site of binding during the initial binding. The rates have been directly used models. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team. For more information see the terms of use . To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
parameter: metaid_0000034
volume units: metaid_0000040
parameter: metaid_0020046
parameter: metaid_0400046
curated: true
length unit: length
parameter: metaid_0000039
units def: metaid_0000032
species: 481311
species: 481291
reaction: metaid_0000048
parameter: metaid_0010046
reaction: metaid_0000047

481231
type: Species
boundary condition: false
initial concentration: 0.0
has part: P19687
has part: CHEBI:16480
constant: false
in compartment: 481131
initial amount: NaN
has part: P16068
has only substance units: false
is: SBO:0000297

481131
type: Compartment
is: GO:0005829
constant: true
size: 1.0
spatial dimensions: 3.0

metaid_0000038
type: Parameter
constant: true
units: metaid_0000035
value: 20.0
name: k4

389746
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

metaid_0000045
type: Parameter
constant: true
units: metaid_0000035
value: 1.6
name: k11

481211
type: Species
has version: P16068
in compartment: 481131
has version: P19687
boundary condition: false
initial amount: NaN
has only substance units: false
initial concentration: 0.112
constant: false
is: SBO:0000297

metaid_0300046
type: Parameter
notes: micromolar extinction coefficient of the 5-coordinate ferrous nitrosyl species at 431 nm
constant: true
units: metaid_0020031
value: 0.025
name: ext_5coord_NO

389782
type: SBMLUnit
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE

389770
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE

389758
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

389709
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

389697
type: SBMLUnit
exponent: -1.0
scale: -6
multipler: 1.0
kind: MOLE

389685
type: SBMLUnit
exponent: 1.0
scale: 0
multipler: 1.0
kind: LITRE

481351
type: Species
initial concentration: 0.288
boundary condition: false
has only substance units: false
is: SBO:0000297
constant: false
initial amount: NaN
has part: P19687
in compartment: 481131
has part: P16068

metaid_0000036
type: Parameter
constant: true
units: metaid_0000035
value: 800.0
name: k2

metaid_0000042
type: Parameter
constant: true
units: metaid_0000035
value: 850.0
name: k8

metaid_0000052
type: Reaction
kinetic law: 390049
product: 390037
reactant: 390025
reactant: 390012
is: SBO:0000177
fast: false
reversible: true
name: r3slow

390037
type: SpeciesReference
stoichiometry: 1.0
species: 481291

481291
type: Species
has part: P16068
constant: false
boundary condition: false
initial concentration: 0.0
has part: CHEBI:16480
has part: P19687
initial amount: NaN
has only substance units: false
is: SBO:0000297
in compartment: 481131

390025
type: SpeciesReference
stoichiometry: 1.0
species: 481311

481311
type: Species
boundary condition: false
initial concentration: 0.0
has part: P19687
has part: P16068
constant: false
initial amount: NaN
has only substance units: false
is: SBO:0000297
in compartment: 481131
has part: CHEBI:16480

390012
type: SpeciesReference
stoichiometry: 1.0
species: 481391

481391
type: Species
has only substance units: false
constant: false
initial concentration: 0.5
in compartment: 481131
is: CHEBI:16480
is: SBO:0000247
is: C00533
boundary condition: true
initial amount: NaN

481191
type: Species
has part: CHEBI:16480
has part: P16068
has part: P19687
boundary condition: false
has only substance units: false
initial concentration: 0.0
in compartment: 481131
is: SBO:0000297
initial amount: NaN
constant: false

metaid_0500046
type: Parameter
notes: extinction at 431 nm
constant: false
units: metaid_0010031
value: NaN
name: extinction

389794
type: SBMLUnit
exponent: -1.0
scale: -2
multipler: 1.0
kind: METRE

metaid_0000041
type: Parameter
constant: true
units: metaid_0000035
value: 800.0
name: k7

481271
type: Species
boundary condition: false
initial concentration: 0.0
has part: P19687
initial amount: NaN
constant: false
is: SBO:0000297
has part: P16068
has only substance units: false
has part: CHEBI:16480
in compartment: 481131

metaid_0000044
type: Parameter
constant: true
units: metaid_0000035
value: 25.0
name: k10

metaid_0000037
type: Parameter
constant: true
units: metaid_0000035
value: 850.0
name: k3

metaid_0000053
type: Reaction
kinetic law: 390085
product: 390073
reactant: 390061
is: SBO:0000181
fast: false
reversible: true
name: r4slow

390073
type: SpeciesReference
stoichiometry: 1.0
species: 481271

390061
type: SpeciesReference
stoichiometry: 1.0
species: 481291

482411
type: Species
in compartment: 481131
has part: P19687
is: SBO:0000297
has part: P16068
boundary condition: false
has part: CHEBI:16480
initial amount: NaN
has only substance units: false
constant: false
initial concentration: 0.0

481171
type: Species
has part: CHEBI:16480
initial concentration: 0.0
in compartment: 481131
has part: P16068
has part: P19687
is: SBO:0000297
has only substance units: false
constant: false
boundary condition: false
initial amount: NaN

metaid_0000040
type: Parameter
constant: true
units: metaid_0000031
value: 700.0
name: k6

metaid_0000043
type: Parameter
constant: true
units: metaid_0000031
value: 5.0
name: k9

metaid_0000051
type: Reaction
kinetic law: 390000
product: 389988
reactant: 389976
is: SBO:0000181
fast: false
reversible: false
name: r2slow

389988
type: SpeciesReference
stoichiometry: 1.0
species: 481311

389976
type: SpeciesReference
stoichiometry: 1.0
species: 481331

481331
type: Species
has part: P19687
has part: P16068
is: SBO:0000297
in compartment: 481131
initial amount: NaN
boundary condition: false
has only substance units: false
initial concentration: 0.0
constant: false
has part: CHEBI:16480

metaid_0000049
type: Reaction
kinetic law: 389915
product: 389903
reactant: 389891
is: SBO:0000181
fast: false
reversible: true
name: r3fast

389903
type: SpeciesReference
stoichiometry: 1.0
species: 481231

389891
type: SpeciesReference
stoichiometry: 1.0
species: 481191

metaid_0000030
type: SBMLUnitsDef
unit: 389673
name: micromole

389673
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

481411
type: Species
has part: CHEBI:16480
is: SBO:0000297
in compartment: 481131
has part: P19687
initial concentration: 0.0
has only substance units: false
constant: false
boundary condition: false
initial amount: NaN
has part: P16068

metaid_0000050
type: Reaction
kinetic law: 389963
product: 389951
reactant: 389939
reactant: 389927
is: SBO:0000177
fast: false
reversible: true
name: r1slow

389951
type: SpeciesReference
stoichiometry: 1.0
species: 481331

389939
type: SpeciesReference
stoichiometry: 1.0
species: 481351

389927
type: SpeciesReference
stoichiometry: 1.0
species: 481391

metaid_0000034
type: Parameter
constant: true
units: metaid_0000031
value: 700.0
name: k1

metaid_0020046
type: Parameter
notes: micromolar extinction coefficient of the 5-coordinate ferrous species at 431 nm
constant: true
units: metaid_0020031
value: 0.11
name: ext_5coord

metaid_0400046
type: Parameter
notes: micromolar extinction coefficient of the 6-coordinate ferrous nitrosyl species at 431 nm
constant: true
units: metaid_0020031
value: 0.064
name: ext_6coord_NO

metaid_0000039
type: Parameter
constant: true
units: metaid_0000035
value: 0.2
name: k5

389733
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: LITRE

389721
type: SBMLUnit
exponent: 1.0
scale: -6
multipler: 1.0
kind: MOLE

metaid_0000048
type: Reaction
kinetic law: 389879
product: 389866
reactant: 389854
is: SBO:0000181
fast: false
reversible: false
name: r2fast

389866
type: SpeciesReference
stoichiometry: 1.0
species: 481191

389854
type: SpeciesReference
stoichiometry: 1.0
species: 481171

metaid_0010046
type: Parameter
constant: true
units: metaid_0000035
value: 0.02
name: k12

metaid_0000047
type: Reaction
kinetic law: 389842
product: 389830
reactant: 389818
reactant: 389806
is: SBO:0000177
fast: false
reversible: true
name: r1fast

389830
type: SpeciesReference
stoichiometry: 1.0
species: 481171

389818
type: SpeciesReference
stoichiometry: 1.0
species: 481211

389806
type: SpeciesReference
stoichiometry: 1.0
species: 481391