2BCG

Structure of doubly prenylated Ypt1:GDI complex

Functional Information from GO Data

Chain	GOid	namespace	contents
G	0005092	molecular_function	GDP-dissociation inhibitor activity
G	0005093	molecular_function	Rab GDP-dissociation inhibitor activity
G	0005096	molecular_function	GTPase activator activity
G	0005515	molecular_function	protein binding
G	0005575	cellular_component	cellular_component
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0007264	biological_process	small GTPase-mediated signal transduction
G	0015031	biological_process	protein transport
G	0016192	biological_process	vesicle-mediated transport
Y	0000045	biological_process	autophagosome assembly
Y	0000139	cellular_component	Golgi membrane
Y	0000149	molecular_function	SNARE binding
Y	0000166	molecular_function	nucleotide binding
Y	0000407	cellular_component	phagophore assembly site
Y	0003924	molecular_function	GTPase activity
Y	0005515	molecular_function	protein binding
Y	0005525	molecular_function	GTP binding
Y	0005737	cellular_component	cytoplasm
Y	0005739	cellular_component	mitochondrion
Y	0005783	cellular_component	endoplasmic reticulum
Y	0005789	cellular_component	endoplasmic reticulum membrane
Y	0005794	cellular_component	Golgi apparatus
Y	0005795	cellular_component	Golgi stack
Y	0005801	cellular_component	cis-Golgi network
Y	0005829	cellular_component	cytosol
Y	0006886	biological_process	intracellular protein transport
Y	0006888	biological_process	endoplasmic reticulum to Golgi vesicle-mediated transport
Y	0006890	biological_process	retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum
Y	0006914	biological_process	autophagy
Y	0012505	cellular_component	endomembrane system
Y	0015031	biological_process	protein transport
Y	0016020	cellular_component	membrane
Y	0016192	biological_process	vesicle-mediated transport
Y	0016236	biological_process	macroautophagy
Y	0031410	cellular_component	cytoplasmic vesicle
Y	0032258	biological_process	cytoplasm to vacuole targeting by the Cvt pathway
Y	0032456	biological_process	endocytic recycling
Y	0034045	cellular_component	phagophore assembly site membrane
Y	0034497	biological_process	protein localization to phagophore assembly site
Y	0034498	biological_process	early endosome to Golgi transport
Y	0035493	biological_process	SNARE complex assembly
Y	0035494	biological_process	SNARE complex disassembly
Y	0048194	biological_process	Golgi vesicle budding
Y	0048211	biological_process	Golgi vesicle docking
Y	0061709	biological_process	reticulophagy
Y	0090114	biological_process	COPII-coated vesicle budding
Y	1900101	biological_process	regulation of endoplasmic reticulum unfolded protein response
Y	1990261	biological_process	pre-mRNA catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG Y 1208

Chain	Residue
Y	SER22
Y	GDP1207
Y	HOH3243
Y	HOH3244
Y	HOH3245
Y	HOH3246

---

site_id	AC2
Number of Residues	27
Details	BINDING SITE FOR RESIDUE GDP Y 1207

Chain	Residue
Y	LYS21
Y	SER22
Y	CYS23
Y	TYR33
Y	THR34
Y	ASP36
Y	TYR37
Y	ASN121
Y	LYS122
Y	ASP124
Y	LEU125
Y	SER151
Y	ALA152
Y	LEU153
Y	MG1208
Y	HOH3002
Y	HOH3004
Y	HOH3024
Y	HOH3043
Y	HOH3054
Y	HOH3057
Y	HOH3243
Y	HOH3244
Y	HOH3246
Y	GLY18
Y	VAL19
Y	GLY20

---

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GER G 4000

Chain	Residue
G	PRO128
G	ALA134
G	LYS145
G	PHE192
G	CYS221
G	VAL224
G	GER2000

---

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GER G 2000

Chain	Residue
G	ALA134
G	LYS145
G	MET148
G	LEU152
G	ILE155
G	CYS221
G	ASP371
G	GER4000

---

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE TRS Y 3000

Chain	Residue
G	VAL435
G	THR436
G	GLY437
G	HOH4132
G	HOH4259
G	HOH4281
Y	ASP141
Y	HOH3267
Y	HOH3269
Y	HOH3270

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	31
Details	Region: {"description":"Interaction with YPT1","evidences":[{"source":"PubMed","id":"14576435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	23
Details	Region: {"description":"Interaction with GDI1","evidences":[{"source":"PubMed","id":"14576435","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	8
Details	Motif: {"description":"Effector region","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	17
Details	Binding site: {"evidences":[{"source":"PubMed","id":"14576435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16034420","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16395334","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1UKV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1YZN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2BCG","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16034420","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1YZN","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"19779198","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","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
Y	GLN67

---

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

Chain	Residue	Details
Y	GLY18

---