1YND
Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6A resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000413 | biological_process | protein peptidyl-prolyl isomerization |
| A | 0001933 | biological_process | negative regulation of protein phosphorylation |
| A | 0001934 | biological_process | positive regulation of protein phosphorylation |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003755 | molecular_function | peptidyl-prolyl cis-trans isomerase activity |
| A | 0005178 | molecular_function | integrin binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005615 | cellular_component | extracellular space |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0005925 | cellular_component | focal adhesion |
| A | 0006457 | biological_process | protein folding |
| A | 0006469 | biological_process | negative regulation of protein kinase activity |
| A | 0006915 | biological_process | apoptotic process |
| A | 0016018 | molecular_function | cyclosporin A binding |
| A | 0016020 | cellular_component | membrane |
| A | 0016853 | molecular_function | isomerase activity |
| A | 0019076 | biological_process | viral release from host cell |
| A | 0030168 | biological_process | platelet activation |
| A | 0030593 | biological_process | neutrophil chemotaxis |
| A | 0030595 | biological_process | leukocyte chemotaxis |
| A | 0031982 | cellular_component | vesicle |
| A | 0032148 | biological_process | activation of protein kinase B activity |
| A | 0032873 | biological_process | negative regulation of stress-activated MAPK cascade |
| A | 0032991 | cellular_component | protein-containing complex |
| A | 0034389 | biological_process | lipid droplet organization |
| A | 0034599 | biological_process | cellular response to oxidative stress |
| A | 0034774 | cellular_component | secretory granule lumen |
| A | 0042118 | biological_process | endothelial cell activation |
| A | 0043410 | biological_process | positive regulation of MAPK cascade |
| A | 0045069 | biological_process | regulation of viral genome replication |
| A | 0045070 | biological_process | positive regulation of viral genome replication |
| A | 0046790 | molecular_function | virion binding |
| A | 0050714 | biological_process | positive regulation of protein secretion |
| A | 0051082 | molecular_function | unfolded protein binding |
| A | 0051092 | biological_process | positive regulation of NF-kappaB transcription factor activity |
| A | 0060352 | biological_process | cell adhesion molecule production |
| A | 0061944 | biological_process | negative regulation of protein K48-linked ubiquitination |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0070527 | biological_process | platelet aggregation |
| A | 1902176 | biological_process | negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway |
| A | 1903901 | biological_process | negative regulation of viral life cycle |
| A | 1904399 | molecular_function | heparan sulfate binding |
| A | 1904813 | cellular_component | ficolin-1-rich granule lumen |
| A | 2001233 | biological_process | regulation of apoptotic signaling pathway |
| B | 0000413 | biological_process | protein peptidyl-prolyl isomerization |
| B | 0001933 | biological_process | negative regulation of protein phosphorylation |
| B | 0001934 | biological_process | positive regulation of protein phosphorylation |
| B | 0003723 | molecular_function | RNA binding |
| B | 0003755 | molecular_function | peptidyl-prolyl cis-trans isomerase activity |
| B | 0005178 | molecular_function | integrin binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005615 | cellular_component | extracellular space |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0005925 | cellular_component | focal adhesion |
| B | 0006457 | biological_process | protein folding |
| B | 0006469 | biological_process | negative regulation of protein kinase activity |
| B | 0006915 | biological_process | apoptotic process |
| B | 0016018 | molecular_function | cyclosporin A binding |
| B | 0016020 | cellular_component | membrane |
| B | 0016853 | molecular_function | isomerase activity |
| B | 0019076 | biological_process | viral release from host cell |
| B | 0030168 | biological_process | platelet activation |
| B | 0030593 | biological_process | neutrophil chemotaxis |
| B | 0030595 | biological_process | leukocyte chemotaxis |
| B | 0031982 | cellular_component | vesicle |
| B | 0032148 | biological_process | activation of protein kinase B activity |
| B | 0032873 | biological_process | negative regulation of stress-activated MAPK cascade |
| B | 0032991 | cellular_component | protein-containing complex |
| B | 0034389 | biological_process | lipid droplet organization |
| B | 0034599 | biological_process | cellular response to oxidative stress |
| B | 0034774 | cellular_component | secretory granule lumen |
| B | 0042118 | biological_process | endothelial cell activation |
| B | 0043410 | biological_process | positive regulation of MAPK cascade |
| B | 0045069 | biological_process | regulation of viral genome replication |
| B | 0045070 | biological_process | positive regulation of viral genome replication |
| B | 0046790 | molecular_function | virion binding |
| B | 0050714 | biological_process | positive regulation of protein secretion |
| B | 0051082 | molecular_function | unfolded protein binding |
| B | 0051092 | biological_process | positive regulation of NF-kappaB transcription factor activity |
| B | 0060352 | biological_process | cell adhesion molecule production |
| B | 0061944 | biological_process | negative regulation of protein K48-linked ubiquitination |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0070527 | biological_process | platelet aggregation |
| B | 1902176 | biological_process | negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway |
| B | 1903901 | biological_process | negative regulation of viral life cycle |
| B | 1904399 | molecular_function | heparan sulfate binding |
| B | 1904813 | cellular_component | ficolin-1-rich granule lumen |
| B | 2001233 | biological_process | regulation of apoptotic signaling pathway |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE SFA A 401 |
| Chain | Residue |
| A | ARG55 |
| A | GLN111 |
| A | PHE113 |
| A | LEU122 |
| A | HIS126 |
| A | HOH412 |
| A | HOH429 |
| A | HOH583 |
| A | HOH584 |
| A | HOH585 |
| A | HOH586 |
| A | GLY59 |
| B | ALA103 |
| B | GLY104 |
| B | TRP121 |
| B | SFA402 |
| B | HOH451 |
| B | HOH467 |
| A | PHE60 |
| A | MET61 |
| A | GLN63 |
| A | THR73 |
| A | ALA101 |
| A | ASN102 |
| A | ALA103 |
| site_id | AC2 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE SFA B 402 |
| Chain | Residue |
| A | ALA103 |
| A | GLY104 |
| A | TRP121 |
| A | SFA401 |
| A | HOH429 |
| A | HOH584 |
| B | VAL2 |
| B | ARG55 |
| B | GLY59 |
| B | PHE60 |
| B | MET61 |
| B | GLN63 |
| B | THR73 |
| B | ALA101 |
| B | ASN102 |
| B | ALA103 |
| B | GLN111 |
| B | PHE113 |
| B | LEU122 |
| B | LYS125 |
| B | HIS126 |
| B | HOH403 |
| B | HOH404 |
| B | HOH405 |
| B | HOH418 |
| B | HOH478 |
| B | HOH522 |
Functional Information from PROSITE/UniProt
| site_id | PS00170 |
| Number of Residues | 18 |
| Details | CSA_PPIASE_1 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. YkgScFHRIIpgFMcQGG |
| Chain | Residue | Details |
| A | TYR48-GLY65 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 312 |
| Details | Domain: {"description":"PPIase cyclophilin-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00156","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N-acetylvaline; partial; in Peptidyl-prolyl cis-trans isomerase A, N-terminally processed","evidences":[{"source":"PubMed","id":"25489052","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2005","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Claeys D."]}},{"source":"PubMed","id":"19413330","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"25944712","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI7 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"20364129","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25678563","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI8 |
| Number of Residues | 2 |
| Details | Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P17742","evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI9 |
| Number of Residues | 2 |
| Details | Glycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI10 |
| Number of Residues | 2 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate"} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 7 |
| Details | M-CSA 189 |
| Chain | Residue | Details |
| A | ARG55 | electrostatic stabiliser, hydrogen bond donor, steric role |
| A | PHE60 | polar/non-polar interaction, steric role |
| A | GLN63 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| A | ASN102 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| A | PHE113 | polar/non-polar interaction, steric role |
| A | LEU122 | polar/non-polar interaction, steric role |
| A | HIS126 | polar/non-polar interaction, steric role |
| site_id | MCSA2 |
| Number of Residues | 7 |
| Details | M-CSA 189 |
| Chain | Residue | Details |
| B | ARG55 | electrostatic stabiliser, hydrogen bond donor, steric role |
| B | PHE60 | polar/non-polar interaction, steric role |
| B | GLN63 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| B | ASN102 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor |
| B | PHE113 | polar/non-polar interaction, steric role |
| B | LEU122 | polar/non-polar interaction, steric role |
| B | HIS126 | polar/non-polar interaction, steric role |
