Capturing cooperative interactions with the PSI-MI format

ExperimentList
Experiment #30
Name:cheng-2006-1
pubmed16707497 [primary-reference]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:inferred by author
psi-miMI:0363 [identical object]
Participant identification method:
Name:predetermined
psi-miMI:0396 [identical object]
publication year2006
author-listCheng et al.
Experiment #31
Name:stevenson-2002-1
pubmed12081504 [primary-reference]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:inferred by author
psi-miMI:0363 [identical object]
Participant identification method:
Name:predetermined
psi-miMI:0396 [identical object]
publication year2002
author-listStevenson et al.
Experiment #32
Name:jeffrey-1995-1
pubmed7630397 [primary-reference]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:inferred by author
psi-miMI:0363 [identical object]
Participant identification method:
Name:predetermined
psi-miMI:0396 [identical object]
publication year1995
author-listJeffrey et al.
Experiment #33
Name:Brown-1999-1
pubmed10559988 [primary-reference]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:inferred by author
psi-miMI:0363 [identical object]
Participant identification method:
Name:predetermined
psi-miMI:0396 [identical object]
publication year1999
author-listBrown et al.
Experiment #34
Name:russo-1996-1
pubmed8756328 [primary-reference]
Host Organism: in vitro (taxid: -1)
Interaction detection method:
Name:inferred by author
psi-miMI:0363 [identical object]
Participant identification method:
Name:predetermined
psi-miMI:0396 [identical object]
publication year1996
author-listRusso et al.

InteractorList
Interactor #1
Name:Cdk2: Cyclin-dependent kinase 2 (gene name: CDK2) (synonym: p33 protein kinase)
uniprot knowledge baseP24941 [identical object]
refseqNP_001789.2 [identical object]
ensemblENSG00000123374 [gene product]
Interactor Type:
Name:protein
psi-miMI:0326 [identical object]
Organism: Human
Interactor #2
Name:Ccna2: Cyclin-A2 (gene name: CCNA2) (synonym: CCN1)
uniprot knowledge baseP20248 [identical object]
refseqNP_001228.1 [identical object]
ensemblENSG00000145386 [gene product]
Interactor Type:
Name:protein
psi-miMI:0326 [identical object]
Organism: Human
Interactor #3
Name:Cdk7: Cyclin-dependent kinase 7 (gene name: CDK7) (synonym: CDK-activating kinase 1)
uniprot knowledge baseP50613 [identical object]
refseqNP_001790.1 [identical object]
ensemblENSG00000134058 [gene product]
Interactor Type:
Name:protein
psi-miMI:0326 [identical object]
Organism: Human
Interactor #4
Name:Cdc6: Cell division control protein 6 homolog (gene name: CDC6) (synonym: Cdc18-related protein)
uniprot knowledge baseQ99741
refseqNP_001245.1 [identical object]
ensemblENSG00000094804 [gene product]
Interactor Type:
Name:protein
psi-miMI:0326 [identical object]
Organism: Human

InteractionList
Interaction #5
Name:CyclinA-Cdk2
wwpdb1FIN [identical object]
intactEBI-1030422 [identical object]
Experiments:cheng-2006-1
Participants:
Participant #13
Cdk2
Biological Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Participant #14
Ccna2
Biological Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:direct interaction
psi-miMI:0407
Interaction attributes:
cooperative mechanismpre-assembly
affected interactionCyclinA_pCdk2-Cdc6
cooperative effect outcomepositive cooperative effect
pre-assembly responseconfigurational pre-organization
Interaction #6
Name:CyclinA-Cdk2
wwpdb1FIN [identical object]
intactEBI-1030422 [identical object]
Experiments:stevenson-2002-1 jeffrey-1995-1
Participants:
Participant #15
Cdk2
Biological Role:
Name:allosteric molecule
psi-miMI:1159 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Participant #16
Ccna2
Biological Role:
Name:allosteric effector
psi-miMI:1160 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:direct interaction
psi-miMI:0407
Interaction attributes:
cooperative mechanismallostery
affected interactionCyclinA_pCdk2-Cdc6
cooperative effect outcomepositive cooperative effect
allosteric molecule Participant#15
allosteric effector Participant#16
allosteric mechanismallosteric change in structure
allosteric responseallosteric v-type response
allostery typeheterotropic allostery
Interaction #7
Name:CyclinA-Cdk2
wwpdb1FIN [identical object]
intactEBI-1030422 [identical object]
Experiments:stevenson-2002-1 jeffrey-1995-1
Participants:
Participant #17
Cdk2
Biological Role:
Name:allosteric molecule
psi-miMI:1159 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Participant #18
Ccna2
Biological Role:
Name:allosteric effector
psi-miMI:1160 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:direct interaction
psi-miMI:0407
Interaction attributes:
cooperative mechanismallostery
affected interactionCyclinA_pCdk2-Cdc6
cooperative effect outcomepositive cooperative effect
allosteric molecule Participant#17
allosteric effector Participant#18
allosteric mechanismallosteric change in structure
allosteric responseallosteric k-type response
allostery typeheterotropic allostery
Interaction #8
Name:CyclinA-Cdk2
wwpdb1FIN [identical object]
intactEBI-1030422 [identical object]
Experiments:jeffrey-1995-1
Participants:
Participant #19
Cdk2
Biological Role:
Name:allosteric molecule
psi-miMI:1159 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Participant #20
Ccna2
Biological Role:
Name:allosteric effector
psi-miMI:1160 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:direct interaction
psi-miMI:0407
Interaction attributes:
cooperative mechanismallostery
affected interactionCyclinA_Cdk2-Cdk7
affected interactionCyclinA_Cdk2-Cdk7
affected interactionCyclinA_Cdk2-Cdk7
cooperative effect outcomepositive cooperative effect
allosteric molecule Participant#19
allosteric effector Participant#20
allosteric mechanismallosteric change in structure
allosteric responseallosteric k-type response
allostery typeheterotropic allostery
Interaction #9
Name:CyclinA_Cdk2-Cdk7
wwpdb1JST [identical object]
dipDIP57013E [identical object]
Experiments:stevenson-2002-1 Brown-1999-1
Participants:
Participant #21
CyclinA-Cdk2
Biological Role:
Name:enzyme target
psi-miMI:0502 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Feature #50phosphorylated residue () [ 160 .. 160 ]
resulting-ptm
participant-ref Participant#13
Participant #22
Cdk7
Biological Role:
Name:enzyme
psi-miMI:0501 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:phosphorylation reaction
psi-miMI:0217
Interaction attributes:
cooperative mechanismallostery
affected interactionCyclinA_pCdk2-Cdc6
cooperative effect outcomepositive cooperative effect
allosteric molecule Participant#13
allosteric post-translational modification Feature#50
allosteric mechanismallosteric change in structure
allosteric responseallosteric k-type response
allostery typeheterotropic allostery
Interaction #10
Name:CyclinA_Cdk2-Cdk7
wwpdb1JST [identical object]
dipDIP57013E [identical object]
Experiments:stevenson-2002-1 russo-1996-1
Participants:
Participant #23
CyclinA-Cdk2
Biological Role:
Name:enzyme target
psi-miMI:0502 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Feature #51phosphorylated residue () [ 160 .. 160 ]
resulting-ptm
participant-ref Participant#13
Participant #24
Cdk7
Biological Role:
Name:enzyme
psi-miMI:0501 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:phosphorylation reaction
psi-miMI:0217
Interaction attributes:
cooperative mechanismallostery
affected interactionCyclinA_pCdk2-Cdc6
cooperative effect outcomepositive cooperative effect
allosteric molecule Participant#13
allosteric post-translational modification Feature#51
allosteric mechanismallosteric change in structure
allosteric responseallosteric v-type response
allostery typeheterotropic allostery
Interaction #11
Name:CyclinA_Cdk2-Cdk7
wwpdb1JST [identical object]
dipDIP57013E [identical object]
Experiments:cheng-2006-1 Brown-1999-1
Participants:
Participant #25
CyclinA-Cdk2
Biological Role:
Name:enzyme target
psi-miMI:0502 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Feature #52phosphorylated residue () [ 160 .. 160 ]
resulting-ptm
participant-ref Participant#13
Participant #26
Cdk7
Biological Role:
Name:enzyme
psi-miMI:0501 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Interaction Type:
Name:phosphorylation reaction
psi-miMI:0217 [identical object]
Interaction attributes:
cooperative mechanismpre-assembly
affected interactionCyclinA_pCdk2-Cdc6
cooperative effect outcomepositive cooperative effect
pre-assembly responsealtered physicochemical compatibility
Interaction #12
Name:CyclinA_pCdk2-Cdc6
wwpdb2CCI [identical object]
Experiments:cheng-2006-1
Participants:
Participant #27
CyclinA-Cdk2
Biological Role:
Name:enzyme
psi-miMI:0501 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Feature #53phosphorylated residue () [ 160 .. 160 ]
prerequisite-ptm
participant-ref Participant#13
Participant #28
Cdc6
Biological Role:
Name:enzyme target
psi-miMI:0502 [identical object]
Experimental Role:
Name:unspecified role
psi-miMI:0499 [identical object]
Feature #54phosphorylated residue () [ 74 .. 74 ]
resulting-ptm
Interaction Type:
Name:phosphorylation reaction
psi-miMI:0217 [identical object]