1T91

crystal structure of human small GTPase Rab7(GTP)

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	0005739	cellular_component	mitochondrion
A	0005764	cellular_component	lysosome
A	0005765	cellular_component	lysosomal membrane
A	0005770	cellular_component	late endosome
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	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	0032935	molecular_function	sterol sensor activity
A	0032991	cellular_component	protein-containing complex
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	0042632	biological_process	cholesterol homeostasis
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	0061462	biological_process	protein localization to lysosome
A	0061724	biological_process	lipophagy
A	0070062	cellular_component	extracellular exosome
A	0090120	biological_process	lysosome to ER cholesterol transport
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	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	0005739	cellular_component	mitochondrion
B	0005764	cellular_component	lysosome
B	0005765	cellular_component	lysosomal membrane
B	0005770	cellular_component	late endosome
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	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	0032935	molecular_function	sterol sensor activity
B	0032991	cellular_component	protein-containing complex
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	0042632	biological_process	cholesterol homeostasis
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	0061462	biological_process	protein localization to lysosome
B	0061724	biological_process	lipophagy
B	0070062	cellular_component	extracellular exosome
B	0090120	biological_process	lysosome to ER cholesterol transport
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	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	0000045	biological_process	autophagosome assembly
C	0000166	molecular_function	nucleotide binding
C	0000421	cellular_component	autophagosome membrane
C	0003924	molecular_function	GTPase activity
C	0003925	molecular_function	G protein activity
C	0005515	molecular_function	protein binding
C	0005525	molecular_function	GTP binding
C	0005739	cellular_component	mitochondrion
C	0005764	cellular_component	lysosome
C	0005765	cellular_component	lysosomal membrane
C	0005770	cellular_component	late endosome
C	0005811	cellular_component	lipid droplet
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006622	biological_process	protein targeting to lysosome
C	0006629	biological_process	lipid metabolic process
C	0006897	biological_process	endocytosis
C	0006914	biological_process	autophagy
C	0007174	biological_process	epidermal growth factor catabolic process
C	0008333	biological_process	endosome to lysosome transport
C	0009617	biological_process	response to bacterium
C	0010008	cellular_component	endosome membrane
C	0015031	biological_process	protein transport
C	0016042	biological_process	lipid catabolic process
C	0016787	molecular_function	hydrolase activity
C	0019003	molecular_function	GDP binding
C	0019076	biological_process	viral release from host cell
C	0022615	biological_process	protein to membrane docking
C	0030667	cellular_component	secretory granule membrane
C	0030670	cellular_component	phagocytic vesicle membrane
C	0030672	cellular_component	synaptic vesicle membrane
C	0030904	cellular_component	retromer complex
C	0031267	molecular_function	small GTPase binding
C	0031410	cellular_component	cytoplasmic vesicle
C	0031902	cellular_component	late endosome membrane
C	0031966	cellular_component	mitochondrial membrane
C	0032935	molecular_function	sterol sensor activity
C	0032991	cellular_component	protein-containing complex
C	0033162	cellular_component	melanosome membrane
C	0034045	cellular_component	phagophore assembly site membrane
C	0036466	biological_process	synaptic vesicle recycling via endosome
C	0042147	biological_process	retrograde transport, endosome to Golgi
C	0042632	biological_process	cholesterol homeostasis
C	0045022	biological_process	early endosome to late endosome transport
C	0045335	cellular_component	phagocytic vesicle
C	0045453	biological_process	bone resorption
C	0045732	biological_process	positive regulation of protein catabolic process
C	0048524	biological_process	positive regulation of viral process
C	0061462	biological_process	protein localization to lysosome
C	0061724	biological_process	lipophagy
C	0070062	cellular_component	extracellular exosome
C	0090120	biological_process	lysosome to ER cholesterol transport
C	0090382	biological_process	phagosome maturation
C	0090383	biological_process	phagosome acidification
C	0090385	biological_process	phagosome-lysosome fusion
C	0097208	cellular_component	alveolar lamellar body
C	0098588	cellular_component	bounding membrane of organelle
C	0098830	cellular_component	presynaptic endosome
C	0099638	biological_process	endosome to plasma membrane protein transport
C	1903542	biological_process	negative regulation of exosomal secretion
C	1903543	biological_process	positive regulation of exosomal secretion
C	1905366	biological_process	negative regulation of intralumenal vesicle formation
C	1905394	molecular_function	retromer complex binding
D	0000045	biological_process	autophagosome assembly
D	0000166	molecular_function	nucleotide binding
D	0000421	cellular_component	autophagosome membrane
D	0003924	molecular_function	GTPase activity
D	0003925	molecular_function	G protein activity
D	0005515	molecular_function	protein binding
D	0005525	molecular_function	GTP binding
D	0005739	cellular_component	mitochondrion
D	0005764	cellular_component	lysosome
D	0005765	cellular_component	lysosomal membrane
D	0005770	cellular_component	late endosome
D	0005811	cellular_component	lipid droplet
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006622	biological_process	protein targeting to lysosome
D	0006629	biological_process	lipid metabolic process
D	0006897	biological_process	endocytosis
D	0006914	biological_process	autophagy
D	0007174	biological_process	epidermal growth factor catabolic process
D	0008333	biological_process	endosome to lysosome transport
D	0009617	biological_process	response to bacterium
D	0010008	cellular_component	endosome membrane
D	0015031	biological_process	protein transport
D	0016042	biological_process	lipid catabolic process
D	0016787	molecular_function	hydrolase activity
D	0019003	molecular_function	GDP binding
D	0019076	biological_process	viral release from host cell
D	0022615	biological_process	protein to membrane docking
D	0030667	cellular_component	secretory granule membrane
D	0030670	cellular_component	phagocytic vesicle membrane
D	0030672	cellular_component	synaptic vesicle membrane
D	0030904	cellular_component	retromer complex
D	0031267	molecular_function	small GTPase binding
D	0031410	cellular_component	cytoplasmic vesicle
D	0031902	cellular_component	late endosome membrane
D	0031966	cellular_component	mitochondrial membrane
D	0032935	molecular_function	sterol sensor activity
D	0032991	cellular_component	protein-containing complex
D	0033162	cellular_component	melanosome membrane
D	0034045	cellular_component	phagophore assembly site membrane
D	0036466	biological_process	synaptic vesicle recycling via endosome
D	0042147	biological_process	retrograde transport, endosome to Golgi
D	0042632	biological_process	cholesterol homeostasis
D	0045022	biological_process	early endosome to late endosome transport
D	0045335	cellular_component	phagocytic vesicle
D	0045453	biological_process	bone resorption
D	0045732	biological_process	positive regulation of protein catabolic process
D	0048524	biological_process	positive regulation of viral process
D	0061462	biological_process	protein localization to lysosome
D	0061724	biological_process	lipophagy
D	0070062	cellular_component	extracellular exosome
D	0090120	biological_process	lysosome to ER cholesterol transport
D	0090382	biological_process	phagosome maturation
D	0090383	biological_process	phagosome acidification
D	0090385	biological_process	phagosome-lysosome fusion
D	0097208	cellular_component	alveolar lamellar body
D	0098588	cellular_component	bounding membrane of organelle
D	0098830	cellular_component	presynaptic endosome
D	0099638	biological_process	endosome to plasma membrane protein transport
D	1903542	biological_process	negative regulation of exosomal secretion
D	1903543	biological_process	positive regulation of exosomal secretion
D	1905366	biological_process	negative regulation of intralumenal vesicle formation
D	1905394	molecular_function	retromer complex binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 1301

Chain	Residue
A	THR22
A	THR40
A	GTP1401
A	HOH1406

---

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG B 1302

Chain	Residue
B	THR22
B	THR40
B	GTP1402
B	HOH1430

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 1303

Chain	Residue
C	THR40
C	GTP1403
C	HOH1434
C	THR22

---

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG D 1304

Chain	Residue
D	THR22
D	THR40
D	GTP1404
D	HOH1482

---

site_id	AC5
Number of Residues	25
Details	BINDING SITE FOR RESIDUE GTP A 1401

Chain	Residue
A	SER17
A	GLY18
A	VAL19
A	GLY20
A	LYS21
A	THR22
A	SER23
A	PHE33
A	ASN35
A	TYR37
A	THR40
A	GLY66
A	ASN125
A	LYS126
A	ASP128
A	LEU129
A	SER155
A	ALA156
A	LYS157
A	MG1301
A	HOH1406
A	HOH1409
A	HOH1410
A	HOH1425
A	HOH1426

---

site_id	AC6
Number of Residues	23
Details	BINDING SITE FOR RESIDUE GTP B 1402

Chain	Residue
B	SER17
B	GLY18
B	VAL19
B	GLY20
B	LYS21
B	THR22
B	SER23
B	PHE33
B	ASN35
B	TYR37
B	THR40
B	GLY66
B	ASN125
B	LYS126
B	ASP128
B	LEU129
B	SER155
B	ALA156
B	LYS157
B	MG1302
B	HOH1404
B	HOH1411
B	HOH1416

---

site_id	AC7
Number of Residues	24
Details	BINDING SITE FOR RESIDUE GTP C 1403

Chain	Residue
C	SER17
C	GLY18
C	VAL19
C	GLY20
C	LYS21
C	THR22
C	SER23
C	PHE33
C	ASN35
C	TYR37
C	THR40
C	GLY66
C	ASN125
C	LYS126
C	ASP128
C	LEU129
C	SER155
C	ALA156
C	LYS157
C	MG1303
C	HOH1409
C	HOH1411
C	HOH1434
C	HOH1523

---

site_id	AC8
Number of Residues	23
Details	BINDING SITE FOR RESIDUE GTP D 1404

Chain	Residue
D	GLY66
D	ASN125
D	LYS126
D	ASP128
D	LEU129
D	SER155
D	ALA156
D	LYS157
D	MG1304
D	HOH1413
D	HOH1422
D	HOH1440
D	SER17
D	GLY18
D	VAL19
D	GLY20
D	LYS21
D	THR22
D	SER23
D	PHE33
D	ASN35
D	TYR37
D	THR40

---

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	52
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	60
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	8
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	44
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	8
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	8
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	4
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	4
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

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
A	LEU67

---

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
B	LEU67

---

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
C	LEU67

---

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
D	LEU67

---

site_id	CSA5
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
A	GLY18

---

site_id	CSA6
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
B	GLY18

---

site_id	CSA7
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
C	GLY18

---

site_id	CSA8
Number of Residues	1
Details	Annotated By Reference To The Literature 1ksj

Chain	Residue	Details
D	GLY18

---