Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7N9X

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

This is a non-PDB format compatible entry.

Functional Information from GO Data

Chain	GOid	namespace	contents
AAA	0016032	biological_process	viral process
BBB	0016032	biological_process	viral process
CCC	0016032	biological_process	viral process
GGG	0000413	biological_process	protein peptidyl-prolyl isomerization
GGG	0001933	biological_process	negative regulation of protein phosphorylation
GGG	0001934	biological_process	positive regulation of protein phosphorylation
GGG	0003723	molecular_function	RNA binding
GGG	0003755	molecular_function	peptidyl-prolyl cis-trans isomerase activity
GGG	0005178	molecular_function	integrin binding
GGG	0005515	molecular_function	protein binding
GGG	0005576	cellular_component	extracellular region
GGG	0005615	cellular_component	extracellular space
GGG	0005634	cellular_component	nucleus
GGG	0005737	cellular_component	cytoplasm
GGG	0005829	cellular_component	cytosol
GGG	0005925	cellular_component	focal adhesion
GGG	0006457	biological_process	protein folding
GGG	0006469	biological_process	negative regulation of protein kinase activity
GGG	0006915	biological_process	apoptotic process
GGG	0016018	molecular_function	cyclosporin A binding
GGG	0016020	cellular_component	membrane
GGG	0019076	biological_process	viral release from host cell
GGG	0030168	biological_process	platelet activation
GGG	0030182	biological_process	neuron differentiation
GGG	0030593	biological_process	neutrophil chemotaxis
GGG	0030595	biological_process	leukocyte chemotaxis
GGG	0031982	cellular_component	vesicle
GGG	0032148	biological_process	activation of protein kinase B activity
GGG	0032873	biological_process	negative regulation of stress-activated MAPK cascade
GGG	0032991	cellular_component	protein-containing complex
GGG	0034389	biological_process	lipid droplet organization
GGG	0034599	biological_process	cellular response to oxidative stress
GGG	0034774	cellular_component	secretory granule lumen
GGG	0035307	biological_process	positive regulation of protein dephosphorylation
GGG	0042118	biological_process	endothelial cell activation
GGG	0043410	biological_process	positive regulation of MAPK cascade
GGG	0045069	biological_process	regulation of viral genome replication
GGG	0045070	biological_process	positive regulation of viral genome replication
GGG	0046790	molecular_function	virion binding
GGG	0050714	biological_process	positive regulation of protein secretion
GGG	0051082	molecular_function	unfolded protein binding
GGG	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
GGG	0060352	biological_process	cell adhesion molecule production
GGG	0061944	biological_process	negative regulation of protein K48-linked ubiquitination
GGG	0070062	cellular_component	extracellular exosome
GGG	0070527	biological_process	platelet aggregation
GGG	1902176	biological_process	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
GGG	1903901	biological_process	negative regulation of viral life cycle
GGG	1904399	molecular_function	heparan sulfate binding
GGG	1904813	cellular_component	ficolin-1-rich granule lumen
GGG	2001233	biological_process	regulation of apoptotic signaling pathway
HHH	0000413	biological_process	protein peptidyl-prolyl isomerization
HHH	0001933	biological_process	negative regulation of protein phosphorylation
HHH	0001934	biological_process	positive regulation of protein phosphorylation
HHH	0003723	molecular_function	RNA binding
HHH	0003755	molecular_function	peptidyl-prolyl cis-trans isomerase activity
HHH	0005178	molecular_function	integrin binding
HHH	0005515	molecular_function	protein binding
HHH	0005576	cellular_component	extracellular region
HHH	0005615	cellular_component	extracellular space
HHH	0005634	cellular_component	nucleus
HHH	0005737	cellular_component	cytoplasm
HHH	0005829	cellular_component	cytosol
HHH	0005925	cellular_component	focal adhesion
HHH	0006457	biological_process	protein folding
HHH	0006469	biological_process	negative regulation of protein kinase activity
HHH	0006915	biological_process	apoptotic process
HHH	0016018	molecular_function	cyclosporin A binding
HHH	0016020	cellular_component	membrane
HHH	0019076	biological_process	viral release from host cell
HHH	0030168	biological_process	platelet activation
HHH	0030182	biological_process	neuron differentiation
HHH	0030593	biological_process	neutrophil chemotaxis
HHH	0030595	biological_process	leukocyte chemotaxis
HHH	0031982	cellular_component	vesicle
HHH	0032148	biological_process	activation of protein kinase B activity
HHH	0032873	biological_process	negative regulation of stress-activated MAPK cascade
HHH	0032991	cellular_component	protein-containing complex
HHH	0034389	biological_process	lipid droplet organization
HHH	0034599	biological_process	cellular response to oxidative stress
HHH	0034774	cellular_component	secretory granule lumen
HHH	0035307	biological_process	positive regulation of protein dephosphorylation
HHH	0042118	biological_process	endothelial cell activation
HHH	0043410	biological_process	positive regulation of MAPK cascade
HHH	0045069	biological_process	regulation of viral genome replication
HHH	0045070	biological_process	positive regulation of viral genome replication
HHH	0046790	molecular_function	virion binding
HHH	0050714	biological_process	positive regulation of protein secretion
HHH	0051082	molecular_function	unfolded protein binding
HHH	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
HHH	0060352	biological_process	cell adhesion molecule production
HHH	0061944	biological_process	negative regulation of protein K48-linked ubiquitination
HHH	0070062	cellular_component	extracellular exosome
HHH	0070527	biological_process	platelet aggregation
HHH	1902176	biological_process	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
HHH	1903901	biological_process	negative regulation of viral life cycle
HHH	1904399	molecular_function	heparan sulfate binding
HHH	1904813	cellular_component	ficolin-1-rich granule lumen
HHH	2001233	biological_process	regulation of apoptotic signaling pathway
III	0000413	biological_process	protein peptidyl-prolyl isomerization
III	0001933	biological_process	negative regulation of protein phosphorylation
III	0001934	biological_process	positive regulation of protein phosphorylation
III	0003723	molecular_function	RNA binding
III	0003755	molecular_function	peptidyl-prolyl cis-trans isomerase activity
III	0005178	molecular_function	integrin binding
III	0005515	molecular_function	protein binding
III	0005576	cellular_component	extracellular region
III	0005615	cellular_component	extracellular space
III	0005634	cellular_component	nucleus
III	0005737	cellular_component	cytoplasm
III	0005829	cellular_component	cytosol
III	0005925	cellular_component	focal adhesion
III	0006457	biological_process	protein folding
III	0006469	biological_process	negative regulation of protein kinase activity
III	0006915	biological_process	apoptotic process
III	0016018	molecular_function	cyclosporin A binding
III	0016020	cellular_component	membrane
III	0019076	biological_process	viral release from host cell
III	0030168	biological_process	platelet activation
III	0030182	biological_process	neuron differentiation
III	0030593	biological_process	neutrophil chemotaxis
III	0030595	biological_process	leukocyte chemotaxis
III	0031982	cellular_component	vesicle
III	0032148	biological_process	activation of protein kinase B activity
III	0032873	biological_process	negative regulation of stress-activated MAPK cascade
III	0032991	cellular_component	protein-containing complex
III	0034389	biological_process	lipid droplet organization
III	0034599	biological_process	cellular response to oxidative stress
III	0034774	cellular_component	secretory granule lumen
III	0035307	biological_process	positive regulation of protein dephosphorylation
III	0042118	biological_process	endothelial cell activation
III	0043410	biological_process	positive regulation of MAPK cascade
III	0045069	biological_process	regulation of viral genome replication
III	0045070	biological_process	positive regulation of viral genome replication
III	0046790	molecular_function	virion binding
III	0050714	biological_process	positive regulation of protein secretion
III	0051082	molecular_function	unfolded protein binding
III	0051092	biological_process	positive regulation of NF-kappaB transcription factor activity
III	0060352	biological_process	cell adhesion molecule production
III	0061944	biological_process	negative regulation of protein K48-linked ubiquitination
III	0070062	cellular_component	extracellular exosome
III	0070527	biological_process	platelet aggregation
III	1902176	biological_process	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway
III	1903901	biological_process	negative regulation of viral life cycle
III	1904399	molecular_function	heparan sulfate binding
III	1904813	cellular_component	ficolin-1-rich granule lumen
III	2001233	biological_process	regulation of apoptotic signaling pathway

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
GGG	TYR48-GLY65

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:22223895, ECO:0007744\|PubMed:22814378, ECO:0007744\|PubMed:25944712

Chain	Residue	Details
GGG	MET1
HHH	MET1
III	MET1

site_id	SWS_FT_FI2
Number of Residues	3
Details	MOD_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

Chain	Residue	Details
GGG	VAL2
HHH	VAL2
III	VAL2

site_id	SWS_FT_FI3
Number of Residues	6
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
GGG	LYS28
GGG	LYS82
HHH	LYS28
HHH	LYS82
III	LYS28
III	LYS82

site_id	SWS_FT_FI4
Number of Residues	9
Details	MOD_RES: N6-acetyllysine => ECO:0007744\|PubMed:19608861

Chain	Residue	Details
GGG	LYS44
GGG	LYS76
GGG	LYS131
HHH	LYS44
HHH	LYS76
HHH	LYS131
III	LYS44
III	LYS76
III	LYS131

site_id	SWS_FT_FI5
Number of Residues	3
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
GGG	SER77
HHH	SER77
III	SER77

site_id	SWS_FT_FI6
Number of Residues	3
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:20068231

Chain	Residue	Details
GGG	THR93
HHH	THR93
III	THR93

site_id	SWS_FT_FI7
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:20364129, ECO:0000269\|PubMed:25678563, ECO:0007744\|PubMed:19608861

Chain	Residue	Details
GGG	LYS125
HHH	LYS125
III	LYS125

site_id	SWS_FT_FI8
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:P17742

Chain	Residue	Details
GGG	LYS133
HHH	LYS133
III	LYS133

site_id	SWS_FT_FI9
Number of Residues	3
Details	CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000255

Chain	Residue	Details
GGG	ASN108
HHH	ASN108
III	ASN108

site_id	SWS_FT_FI10
Number of Residues	3
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate

Chain	Residue	Details
GGG	LYS28
HHH	LYS28
III	LYS28

site_id	SWS_FT_FI11
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
GGG	LYS82
HHH	LYS82
III	LYS82

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	7
Details	M-CSA 189

Chain	Residue	Details
GGG	ARG55	electrostatic stabiliser, hydrogen bond donor, steric role
GGG	PHE60	polar/non-polar interaction, steric role
GGG	GLN63	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
GGG	ASN102	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
GGG	PHE113	polar/non-polar interaction, steric role
GGG	LEU122	polar/non-polar interaction, steric role
GGG	HIS126	polar/non-polar interaction, steric role

site_id	MCSA2
Number of Residues	7
Details	M-CSA 189

Chain	Residue	Details
HHH	ARG55	electrostatic stabiliser, hydrogen bond donor, steric role
HHH	PHE60	polar/non-polar interaction, steric role
HHH	GLN63	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
HHH	ASN102	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
HHH	PHE113	polar/non-polar interaction, steric role
HHH	LEU122	polar/non-polar interaction, steric role
HHH	HIS126	polar/non-polar interaction, steric role

site_id	MCSA3
Number of Residues	7
Details	M-CSA 189

Chain	Residue	Details
III	ARG55	electrostatic stabiliser, hydrogen bond donor, steric role
III	PHE60	polar/non-polar interaction, steric role
III	GLN63	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
III	ASN102	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor
III	PHE113	polar/non-polar interaction, steric role
III	LEU122	polar/non-polar interaction, steric role
III	HIS126	polar/non-polar interaction, steric role

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)