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1YND

Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6A resolution

Functional Information from GO Data
ChainGOidnamespacecontents
A0000413biological_processprotein peptidyl-prolyl isomerization
A0001933biological_processnegative regulation of protein phosphorylation
A0001934biological_processpositive regulation of protein phosphorylation
A0003723molecular_functionRNA binding
A0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
A0005178molecular_functionintegrin binding
A0005515molecular_functionprotein binding
A0005576cellular_componentextracellular region
A0005615cellular_componentextracellular space
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0005925cellular_componentfocal adhesion
A0006457biological_processprotein folding
A0006469biological_processnegative regulation of protein kinase activity
A0006915biological_processapoptotic process
A0016018molecular_functioncyclosporin A binding
A0016020cellular_componentmembrane
A0019076biological_processviral release from host cell
A0030168biological_processplatelet activation
A0030182biological_processneuron differentiation
A0030593biological_processneutrophil chemotaxis
A0030595biological_processleukocyte chemotaxis
A0031982cellular_componentvesicle
A0032148biological_processactivation of protein kinase B activity
A0032873biological_processnegative regulation of stress-activated MAPK cascade
A0032991cellular_componentprotein-containing complex
A0034389biological_processlipid droplet organization
A0034599biological_processcellular response to oxidative stress
A0034774cellular_componentsecretory granule lumen
A0035307biological_processpositive regulation of protein dephosphorylation
A0042118biological_processendothelial cell activation
A0043410biological_processpositive regulation of MAPK cascade
A0045069biological_processregulation of viral genome replication
A0045070biological_processpositive regulation of viral genome replication
A0046790molecular_functionvirion binding
A0050714biological_processpositive regulation of protein secretion
A0051082molecular_functionunfolded protein binding
A0051092biological_processpositive regulation of NF-kappaB transcription factor activity
A0060352biological_processcell adhesion molecule production
A0061944biological_processnegative regulation of protein K48-linked ubiquitination
A0070062cellular_componentextracellular exosome
A0070527biological_processplatelet aggregation
A1902176biological_processnegative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
A1903901biological_processnegative regulation of viral life cycle
A1904399molecular_functionheparan sulfate binding
A1904813cellular_componentficolin-1-rich granule lumen
A2001233biological_processregulation of apoptotic signaling pathway
B0000413biological_processprotein peptidyl-prolyl isomerization
B0001933biological_processnegative regulation of protein phosphorylation
B0001934biological_processpositive regulation of protein phosphorylation
B0003723molecular_functionRNA binding
B0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
B0005178molecular_functionintegrin binding
B0005515molecular_functionprotein binding
B0005576cellular_componentextracellular region
B0005615cellular_componentextracellular space
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0005925cellular_componentfocal adhesion
B0006457biological_processprotein folding
B0006469biological_processnegative regulation of protein kinase activity
B0006915biological_processapoptotic process
B0016018molecular_functioncyclosporin A binding
B0016020cellular_componentmembrane
B0019076biological_processviral release from host cell
B0030168biological_processplatelet activation
B0030182biological_processneuron differentiation
B0030593biological_processneutrophil chemotaxis
B0030595biological_processleukocyte chemotaxis
B0031982cellular_componentvesicle
B0032148biological_processactivation of protein kinase B activity
B0032873biological_processnegative regulation of stress-activated MAPK cascade
B0032991cellular_componentprotein-containing complex
B0034389biological_processlipid droplet organization
B0034599biological_processcellular response to oxidative stress
B0034774cellular_componentsecretory granule lumen
B0035307biological_processpositive regulation of protein dephosphorylation
B0042118biological_processendothelial cell activation
B0043410biological_processpositive regulation of MAPK cascade
B0045069biological_processregulation of viral genome replication
B0045070biological_processpositive regulation of viral genome replication
B0046790molecular_functionvirion binding
B0050714biological_processpositive regulation of protein secretion
B0051082molecular_functionunfolded protein binding
B0051092biological_processpositive regulation of NF-kappaB transcription factor activity
B0060352biological_processcell adhesion molecule production
B0061944biological_processnegative regulation of protein K48-linked ubiquitination
B0070062cellular_componentextracellular exosome
B0070527biological_processplatelet aggregation
B1902176biological_processnegative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
B1903901biological_processnegative regulation of viral life cycle
B1904399molecular_functionheparan sulfate binding
B1904813cellular_componentficolin-1-rich granule lumen
B2001233biological_processregulation of apoptotic signaling pathway
Functional Information from PDB Data
site_idAC1
Number of Residues25
DetailsBINDING SITE FOR RESIDUE SFA A 401
ChainResidue
AARG55
AGLN111
APHE113
ALEU122
AHIS126
AHOH412
AHOH429
AHOH583
AHOH584
AHOH585
AHOH586
AGLY59
BALA103
BGLY104
BTRP121
BSFA402
BHOH451
BHOH467
APHE60
AMET61
AGLN63
ATHR73
AALA101
AASN102
AALA103

site_idAC2
Number of Residues27
DetailsBINDING SITE FOR RESIDUE SFA B 402
ChainResidue
AALA103
AGLY104
ATRP121
ASFA401
AHOH429
AHOH584
BVAL2
BARG55
BGLY59
BPHE60
BMET61
BGLN63
BTHR73
BALA101
BASN102
BALA103
BGLN111
BPHE113
BLEU122
BLYS125
BHIS126
BHOH403
BHOH404
BHOH405
BHOH418
BHOH478
BHOH522

Functional Information from PROSITE/UniProt
site_idPS00170
Number of Residues18
DetailsCSA_PPIASE_1 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. YkgScFHRIIpgFMcQGG
ChainResidueDetails
ATYR48-GLY65

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsMOD_RES: N-acetylmethionine => ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:22223895, ECO:0007744|PubMed:22814378, ECO:0007744|PubMed:25944712
ChainResidueDetails
AVAL2
BVAL2

site_idSWS_FT_FI2
Number of Residues2
DetailsMOD_RES: N-acetylvaline; partial; in Peptidyl-prolyl cis-trans isomerase A, N-terminally processed => ECO:0000269|PubMed:25489052, ECO:0000269|Ref.12, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:25944712
ChainResidueDetails
AASN3
BASN3

site_idSWS_FT_FI3
Number of Residues4
DetailsMOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861
ChainResidueDetails
AVAL29
APHE83
BVAL29
BPHE83

site_idSWS_FT_FI4
Number of Residues6
DetailsMOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861
ChainResidueDetails
AGLY45
ASER77
AVAL132
BGLY45
BSER77
BVAL132

site_idSWS_FT_FI5
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163
ChainResidueDetails
AILE78
BILE78

site_idSWS_FT_FI6
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:20068231
ChainResidueDetails
AGLY94
BGLY94

site_idSWS_FT_FI7
Number of Residues2
DetailsMOD_RES: N6-acetyllysine => ECO:0000269|PubMed:20364129, ECO:0000269|PubMed:25678563, ECO:0007744|PubMed:19608861
ChainResidueDetails
AHIS126
BHIS126

site_idSWS_FT_FI8
Number of Residues2
DetailsMOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P17742
ChainResidueDetails
AGLU134
BGLU134

site_idSWS_FT_FI9
Number of Residues2
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000255
ChainResidueDetails
AGLY109
BGLY109

site_idSWS_FT_FI10
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate
ChainResidueDetails
AVAL29
BVAL29

site_idSWS_FT_FI11
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733
ChainResidueDetails
APHE83
BPHE83

Catalytic Information from CSA
site_idMCSA1
Number of Residues7
DetailsM-CSA 189
ChainResidueDetails
AILE56electrostatic stabiliser, hydrogen bond donor, steric role
AMET61polar/non-polar interaction, steric role
AGLY64electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
AALA103electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
AILE114polar/non-polar interaction, steric role
AASP123polar/non-polar interaction, steric role
AVAL127polar/non-polar interaction, steric role

site_idMCSA2
Number of Residues7
DetailsM-CSA 189
ChainResidueDetails
BILE56electrostatic stabiliser, hydrogen bond donor, steric role
BMET61polar/non-polar interaction, steric role
BGLY64electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
BALA103electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
BILE114polar/non-polar interaction, steric role
BASP123polar/non-polar interaction, steric role
BVAL127polar/non-polar interaction, steric role

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PDB entries from 2024-09-04

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