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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

6Y9W

Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,8)

Functional Information from GO Data
ChainGOidnamespacecontents
A0016032biological_processviral process
B0016032biological_processviral process
C0016032biological_processviral process
D0016032biological_processviral process
G0016032biological_processviral process
H0016032biological_processviral process
J0000413biological_processprotein peptidyl-prolyl isomerization
J0001933biological_processnegative regulation of protein phosphorylation
J0001934biological_processpositive regulation of protein phosphorylation
J0003723molecular_functionRNA binding
J0003755molecular_functionpeptidyl-prolyl cis-trans isomerase activity
J0005178molecular_functionintegrin binding
J0005515molecular_functionprotein binding
J0005576cellular_componentextracellular region
J0005615cellular_componentextracellular space
J0005634cellular_componentnucleus
J0005737cellular_componentcytoplasm
J0005829cellular_componentcytosol
J0005925cellular_componentfocal adhesion
J0006457biological_processprotein folding
J0006469biological_processnegative regulation of protein kinase activity
J0006915biological_processapoptotic process
J0016018molecular_functioncyclosporin A binding
J0016020cellular_componentmembrane
J0016853molecular_functionisomerase activity
J0019076biological_processviral release from host cell
J0030168biological_processplatelet activation
J0030182biological_processneuron differentiation
J0030593biological_processneutrophil chemotaxis
J0030595biological_processleukocyte chemotaxis
J0031982cellular_componentvesicle
J0032148biological_processactivation of protein kinase B activity
J0032873biological_processnegative regulation of stress-activated MAPK cascade
J0032991cellular_componentprotein-containing complex
J0034389biological_processlipid droplet organization
J0034599biological_processcellular response to oxidative stress
J0034774cellular_componentsecretory granule lumen
J0042118biological_processendothelial cell activation
J0043410biological_processpositive regulation of MAPK cascade
J0045069biological_processregulation of viral genome replication
J0045070biological_processpositive regulation of viral genome replication
J0046790molecular_functionvirion binding
J0050714biological_processpositive regulation of protein secretion
J0051082molecular_functionunfolded protein binding
J0051092biological_processpositive regulation of NF-kappaB transcription factor activity
J0060352biological_processcell adhesion molecule production
J0061944biological_processnegative regulation of protein K48-linked ubiquitination
J0070062cellular_componentextracellular exosome
J0070527biological_processplatelet aggregation
J1902176biological_processnegative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
J1903901biological_processnegative regulation of viral life cycle
J1904399molecular_functionheparan sulfate binding
J1904813cellular_componentficolin-1-rich granule lumen
J2001233biological_processregulation of apoptotic signaling pathway
N0016032biological_processviral process
Y0016032biological_processviral process
d0016032biological_processviral process
e0016032biological_processviral process
j0016032biological_processviral process
k0016032biological_processviral process
Functional Information from PROSITE/UniProt
site_idPS00170
Number of Residues18
DetailsCSA_PPIASE_1 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. YkgScFHRIIpgFMcQGG
ChainResidueDetails
JTYR48-GLY65
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues380
DetailsRegion: {"description":"Interaction with human PPIA/CYPA and NUP153","evidences":[{"source":"UniProtKB","id":"P12497","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues80
DetailsRegion: {"description":"PPIA/CYPA-binding loop"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues10
DetailsModified residue: {"description":"Phosphoserine; by host MAPK1","evidences":[{"source":"UniProtKB","id":"P12493","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues10
DetailsSite: {"description":"Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA","evidences":[{"evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues156
DetailsDomain: {"description":"PPIase cyclophilin-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00156","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues1
DetailsModified 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"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues3
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues1
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues1
DetailsModified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues1
DetailsModified 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"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues1
DetailsModified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P17742","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues1
DetailsGlycosylation: {"description":"N-linked (GlcNAc...) asparagine","evidences":[{"evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI14
Number of Residues1
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate"}
ChainResidueDetails
site_idSWS_FT_FI15
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues7
DetailsM-CSA 189
ChainResidueDetails
GTHR54electrostatic stabiliser, hydrogen bond donor, steric role
GVAL59polar/non-polar interaction, steric role
GHIS62electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
GGLY101electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
GGLN112polar/non-polar interaction, steric role
GASN121polar/non-polar interaction, steric role
GPRO125polar/non-polar interaction, steric role

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PDB entries from 2025-07-23

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