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BIOMD0000000475
area units: area
creator:
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  n:
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    family: Juty
modified:
  W3 CDTF: Mon Oct 07 22:21:45 BST 2013
length unit: length
type: SBMLModel
created:
  W3 CDTF: Fri Sep 06 17:57:28 BST 2013
curated: true
parameter: COPASI3
occurs in: http://identifiers.org/taxonomy/4932
creator:
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  n:
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    family: Falconi
name: Amara2013 - PCNA ubiquitylation in the activation of PRR pathway
creator:
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    orgname: EMBL-EBI
  n:
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    family: Chelliah
notes: Mechanistic model of the Post-Replication Repair (PRR), the pathway involved in the bypass of DNA lesions induced by sunlight exposure and UV radiation. PRR acts through two different mechanisms, activated by mono- and poly-ubiquitylation of the DNA sliding clamp, called Proliferating Cell Nuclear Antigen (PCNA). This model has been defined according to the stochastic formulation of chemical kinetics [Gillespie DT, J Phys Chem 1977, 81(25):2340-2361], which requires to specify the set of molecular species occurring in the pathway and their respective interactions, formally described as a set of biochemical reactions. The volume considered for this system is 1.666667e-17L; this value can be used to convert the model into the deterministic formulation.
is: MODEL1211260000
species: COPASI2
is described by: http://identifiers.org/pubmed/23514624
species: COPASI1
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  n:
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is version of: GO:0006301

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fast: false
reversible: false
name: r06
type: Reaction

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value: 5.0E-6
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http://identifiers.org/biomodels.db/BIOMD0000000475#_907462f7_53d4_4907_89dc_cdea36beb90b
stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000475#_5d8b75d1_57b8_43c5_8156_c9eac6a828c4
constant: true
size: 1.0
spatial dimensions: 3.0
name: compartment
type: Compartment

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constant: false
boundary condition: false
has only substance units: false
initial concentration: 7480.0
initial amount: NaN
name: PCNA
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000475#_8c20ae29_9bde_403b_91e4_2bb2e14500c1
stoichiometry: 1.0
species: COPASI1
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value: 0.01
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http://identifiers.org/biomodels.db/BIOMD0000000475#b7f70dc4_fdb5_4533_9ba2_3782564cdb4c
value: 0.078
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type: LocalParameter

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stoichiometry: 1.0
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constant: false
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initial concentration: 193.0
initial amount: NaN
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stoichiometry: 3.0
type: SpeciesReference

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constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
name: Rad18:Rad18:PCNAonU
type: Species

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exponent: 1.0
scale: 0
multipler: 1.0
kind: DIMENSIONLESS
type: SBMLUnit

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stoichiometry: 1.0
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constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
name: PCNAonU:U
type: Species

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constant: false
boundary condition: false
has only substance units: false
initial concentration: 194.0
initial amount: NaN
name: Rad6
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stoichiometry: 1.0
type: SpeciesReference

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constant: false
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has only substance units: false
initial concentration: 0.0
initial amount: NaN
name: Rad5:PCNAonU
type: Species

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stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000475#d543aaa7_658f_4db6_a496_0f4faf6a5c0f
fast: false
reversible: false
name: r13
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000475#c5b4574f_fab7_47ac_b896_57811f60a04c
value: 1.0E-10
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000475#cf9e2801_1dfc_4250_9377_d1453f297050
fast: false
reversible: false
name: r02
type: Reaction

http://identifiers.org/biomodels.db/BIOMD0000000475#_275e159c_44e7_4723_9d28_b2639b0889a7
value: 5.0E-6
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000475#_1b091a35_691d_47ca_b7bc_1c6e5376a34b
stoichiometry: 1.0
type: SpeciesReference

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stoichiometry: 1.0
type: SpeciesReference

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stoichiometry: 1.0
type: SpeciesReference

http://identifiers.org/biomodels.db/BIOMD0000000475#_561b5cc6_eb9a_4504_95da_dee083b276a1
value: 1.0
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type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000475#b8377f8d_3909_4105_9b2d_cc3eb67059db
stoichiometry: 1.0
type: SpeciesReference

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http://identifiers.org/biomodels.db/BIOMD0000000475#dbed093f_4375_4895_a3f5_14dc6effe277
reversible: false
fast: false
type: Reaction
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http://identifiers.org/biomodels.db/BIOMD0000000475#_1798cca1_8939_43a1_a5bd_b3b86bec8e0e
name: r19
reversible: false
fast: false
type: Reaction

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value: 100000.0
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000475#_0b7f03d0_cafa_4625_ae71_23824c5a3d36
value: 1000.0
name: k1
type: LocalParameter

http://identifiers.org/biomodels.db/BIOMD0000000475#_23c10dfe_600d_440e_9e0d_10261d114792
stoichiometry: 1.0
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http://identifiers.org/biomodels.db/BIOMD0000000475#_3ac4bb32_d941_4abb_910b_2cff831fc0e1
fast: false
reversible: false
name: r24
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fast: false
type: Reaction
name: r11
reversible: false

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stoichiometry: 1.0
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fast: false
reversible: false
name: r17
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stoichiometry: 1.0
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stoichiometry: 1.0
type: SpeciesReference

COPASI1
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
name: Ubc13U:Mms2
type: Species

http://identifiers.org/biomodels.db/BIOMD0000000475#_202e0734_1479_4787_a756_782f949e5f8c
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.0
initial amount: NaN
name: PCNAoff
type: Species