Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

7F6J

Crystal structure of the PDZD8 coiled-coil domain - Rab7 complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000045	biological_process	autophagosome assembly
A	0000166	molecular_function	nucleotide binding
A	0000421	cellular_component	autophagosome membrane
A	0003924	molecular_function	GTPase activity
A	0003925	molecular_function	G protein activity
A	0005515	molecular_function	protein binding
A	0005525	molecular_function	GTP binding
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005764	cellular_component	lysosome
A	0005765	cellular_component	lysosomal membrane
A	0005768	cellular_component	endosome
A	0005770	cellular_component	late endosome
A	0005794	cellular_component	Golgi apparatus
A	0005811	cellular_component	lipid droplet
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006622	biological_process	protein targeting to lysosome
A	0006629	biological_process	lipid metabolic process
A	0006897	biological_process	endocytosis
A	0006914	biological_process	autophagy
A	0007174	biological_process	epidermal growth factor catabolic process
A	0008333	biological_process	endosome to lysosome transport
A	0009617	biological_process	response to bacterium
A	0010008	cellular_component	endosome membrane
A	0015031	biological_process	protein transport
A	0016020	cellular_component	membrane
A	0016042	biological_process	lipid catabolic process
A	0016787	molecular_function	hydrolase activity
A	0019003	molecular_function	GDP binding
A	0019076	biological_process	viral release from host cell
A	0022615	biological_process	protein to membrane docking
A	0030667	cellular_component	secretory granule membrane
A	0030670	cellular_component	phagocytic vesicle membrane
A	0030672	cellular_component	synaptic vesicle membrane
A	0030904	cellular_component	retromer complex
A	0031267	molecular_function	small GTPase binding
A	0031410	cellular_component	cytoplasmic vesicle
A	0031902	cellular_component	late endosome membrane
A	0031966	cellular_component	mitochondrial membrane
A	0033162	cellular_component	melanosome membrane
A	0034045	cellular_component	phagophore assembly site membrane
A	0036466	biological_process	synaptic vesicle recycling via endosome
A	0042147	biological_process	retrograde transport, endosome to Golgi
A	0045022	biological_process	early endosome to late endosome transport
A	0045335	cellular_component	phagocytic vesicle
A	0045453	biological_process	bone resorption
A	0045732	biological_process	positive regulation of protein catabolic process
A	0048524	biological_process	positive regulation of viral process
A	0051650	biological_process	establishment of vesicle localization
A	0061462	biological_process	protein localization to lysosome
A	0061724	biological_process	lipophagy
A	0070062	cellular_component	extracellular exosome
A	0090382	biological_process	phagosome maturation
A	0090383	biological_process	phagosome acidification
A	0090385	biological_process	phagosome-lysosome fusion
A	0097208	cellular_component	alveolar lamellar body
A	0098588	cellular_component	bounding membrane of organelle
A	0098830	cellular_component	presynaptic endosome
A	0098943	biological_process	neurotransmitter receptor transport, postsynaptic endosome to lysosome
A	0098978	cellular_component	glutamatergic synapse
A	0099003	biological_process	vesicle-mediated transport in synapse
A	0099638	biological_process	endosome to plasma membrane protein transport
A	1903542	biological_process	negative regulation of exosomal secretion
A	1903543	biological_process	positive regulation of exosomal secretion
A	1905366	biological_process	negative regulation of intralumenal vesicle formation
A	1905394	molecular_function	retromer complex binding
B	0000045	biological_process	autophagosome assembly
B	0000166	molecular_function	nucleotide binding
B	0000421	cellular_component	autophagosome membrane
B	0003924	molecular_function	GTPase activity
B	0003925	molecular_function	G protein activity
B	0005515	molecular_function	protein binding
B	0005525	molecular_function	GTP binding
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005764	cellular_component	lysosome
B	0005765	cellular_component	lysosomal membrane
B	0005768	cellular_component	endosome
B	0005770	cellular_component	late endosome
B	0005794	cellular_component	Golgi apparatus
B	0005811	cellular_component	lipid droplet
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006622	biological_process	protein targeting to lysosome
B	0006629	biological_process	lipid metabolic process
B	0006897	biological_process	endocytosis
B	0006914	biological_process	autophagy
B	0007174	biological_process	epidermal growth factor catabolic process
B	0008333	biological_process	endosome to lysosome transport
B	0009617	biological_process	response to bacterium
B	0010008	cellular_component	endosome membrane
B	0015031	biological_process	protein transport
B	0016020	cellular_component	membrane
B	0016042	biological_process	lipid catabolic process
B	0016787	molecular_function	hydrolase activity
B	0019003	molecular_function	GDP binding
B	0019076	biological_process	viral release from host cell
B	0022615	biological_process	protein to membrane docking
B	0030667	cellular_component	secretory granule membrane
B	0030670	cellular_component	phagocytic vesicle membrane
B	0030672	cellular_component	synaptic vesicle membrane
B	0030904	cellular_component	retromer complex
B	0031267	molecular_function	small GTPase binding
B	0031410	cellular_component	cytoplasmic vesicle
B	0031902	cellular_component	late endosome membrane
B	0031966	cellular_component	mitochondrial membrane
B	0033162	cellular_component	melanosome membrane
B	0034045	cellular_component	phagophore assembly site membrane
B	0036466	biological_process	synaptic vesicle recycling via endosome
B	0042147	biological_process	retrograde transport, endosome to Golgi
B	0045022	biological_process	early endosome to late endosome transport
B	0045335	cellular_component	phagocytic vesicle
B	0045453	biological_process	bone resorption
B	0045732	biological_process	positive regulation of protein catabolic process
B	0048524	biological_process	positive regulation of viral process
B	0051650	biological_process	establishment of vesicle localization
B	0061462	biological_process	protein localization to lysosome
B	0061724	biological_process	lipophagy
B	0070062	cellular_component	extracellular exosome
B	0090382	biological_process	phagosome maturation
B	0090383	biological_process	phagosome acidification
B	0090385	biological_process	phagosome-lysosome fusion
B	0097208	cellular_component	alveolar lamellar body
B	0098588	cellular_component	bounding membrane of organelle
B	0098830	cellular_component	presynaptic endosome
B	0098943	biological_process	neurotransmitter receptor transport, postsynaptic endosome to lysosome
B	0098978	cellular_component	glutamatergic synapse
B	0099003	biological_process	vesicle-mediated transport in synapse
B	0099638	biological_process	endosome to plasma membrane protein transport
B	1903542	biological_process	negative regulation of exosomal secretion
B	1903543	biological_process	positive regulation of exosomal secretion
B	1905366	biological_process	negative regulation of intralumenal vesicle formation
B	1905394	molecular_function	retromer complex binding
C	0044233	cellular_component	mitochondria-associated endoplasmic reticulum membrane contact site
C	0051560	biological_process	mitochondrial calcium ion homeostasis
C	1990456	biological_process	mitochondrion-endoplasmic reticulum membrane tethering

Functional Information from PROSITE/UniProt

site_id	PS00675
Number of Residues	14
Details	SIGMA54_INTERACT_1 Sigma-54 interaction domain ATP-binding region A signature. VIIlGDSGVGKtsL

Chain	Residue	Details
A	VAL11-LEU24

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	26
Details	Motif: {"description":"Switch 1","evidences":[{"source":"PubMed","id":"15933719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T91","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YHN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
Details	Motif: {"description":"Switch 2","evidences":[{"source":"PubMed","id":"15933719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T91","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YHN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20028791","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"3LAW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	22
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15933719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20028791","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"1T91","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YHN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3LAW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15933719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20028791","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1T91","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YHN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3LAW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15933719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1YHN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15933719","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20028791","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1YHN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3LAW","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by LRRK1","evidences":[{"source":"PubMed","id":"36040231","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"37857821","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	35
Details	Coiled coil: {"evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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