6EKK

Crystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005085	molecular_function	guanyl-nucleotide exchange factor activity
B	0005085	molecular_function	guanyl-nucleotide exchange factor activity
C	0003924	molecular_function	GTPase activity
C	0005525	molecular_function	GTP binding
D	0003924	molecular_function	GTPase activity
D	0005525	molecular_function	GTP binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue SO4 A 401

Chain	Residue
A	LYS6
A	GLN7
A	ASN8

---

site_id	AC2
Number of Residues	3
Details	binding site for residue SO4 A 402

Chain	Residue
A	ASP237
C	PHE45
C	GLN60

---

site_id	AC3
Number of Residues	5
Details	binding site for residue EDO A 403

Chain	Residue
A	TYR222
A	TRP223
A	ARG4
A	GLN82
A	ALA215

---

site_id	AC4
Number of Residues	7
Details	binding site for residue EDO A 404

Chain	Residue
A	TYR110
A	ARG170
A	ASN171
A	GLU174
A	SER205
A	THR208
A	HOH564

---

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO A 405

Chain	Residue
A	ASN171
A	HIS212
A	HOH585
A	HOH638

---

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 B 401

Chain	Residue
B	ASN70
B	ASN114
B	HOH525

---

site_id	AC7
Number of Residues	4
Details	binding site for residue SO4 B 402

Chain	Residue
B	LYS6
B	GLN7
B	ASN8
B	LYS81

---

site_id	AC8
Number of Residues	6
Details	binding site for residue SO4 B 403

Chain	Residue
B	GLU45
B	VAL46
B	THR49
B	ARG83
D	THR39
D	THR40

---

site_id	AC9
Number of Residues	5
Details	binding site for residue EDO B 404

Chain	Residue
B	GLN82
B	ALA215
B	TYR222
B	TRP223
B	TYR227

---

site_id	AD1
Number of Residues	2
Details	binding site for residue EDO B 405

Chain	Residue
A	THR272
B	ARG123

---

site_id	AD2
Number of Residues	7
Details	binding site for residue EDO B 406

Chain	Residue
B	ASN70
B	TYR110
B	ARG170
B	ASN171
B	SER205
B	THR208
B	HOH571

---

site_id	AD3
Number of Residues	5
Details	binding site for residue EDO B 407

Chain	Residue
B	PHE337
B	GLU339
B	LYS365
B	HOH526
B	HOH572

---

site_id	AD4
Number of Residues	3
Details	binding site for residue SO4 C 201

Chain	Residue
C	LYS100
C	HIS104
C	HOH343

---

site_id	AD5
Number of Residues	5
Details	binding site for residue SO4 C 202

Chain	Residue
C	ASN31
C	THR32
C	PHE33
C	HOH374
C	HOH381

---

site_id	AD6
Number of Residues	3
Details	binding site for residue EDO C 203

Chain	Residue
A	HOH634
C	PHE33
C	SER36

---

site_id	AD7
Number of Residues	15
Details	binding site for residue GDP C 204

Chain	Residue
C	GLY18
C	VAL19
C	GLY20
C	LYS21
C	SER22
C	SER23
C	ASN120
C	LYS121
C	ASP123
C	SER150
C	ALA151
C	LYS152
C	HOH306
C	HOH312
C	HOH376

---

site_id	AD8
Number of Residues	5
Details	binding site for residue SO4 D 201

Chain	Residue
D	CYS114
D	ARG115
D	GLY143
D	ILE144
D	HOH322

---

site_id	AD9
Number of Residues	5
Details	binding site for residue SO4 D 202

Chain	Residue
B	ILE78
D	SER36
D	THR39
D	GDP203
D	HOH371

---

site_id	AE1
Number of Residues	19
Details	binding site for residue GDP D 203

Chain	Residue
D	SER150
D	ALA151
D	LYS152
D	SO4202
D	HOH312
D	HOH321
D	HOH333
D	HOH384
D	HOH402
D	HOH410
D	GLY18
D	VAL19
D	GLY20
D	LYS21
D	SER22
D	SER23
D	ASN120
D	LYS121
D	ASP123

---

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. LLIiGDSGVGKssL

Chain	Residue	Details
C	LEU11-LEU24

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	272
Details	Domain: {"description":"cDENN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00304","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	156
Details	Domain: {"description":"dDENN","evidences":[{"source":"PROSITE-ProRule","id":"PRU00304","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	8
Details	Motif: {"description":"FXDXF motif","evidences":[{"source":"PubMed","id":"20154091","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	24
Details	Motif: {"description":"Switch 1","evidences":[{"source":"PubMed","id":"30905672","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6IF2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6IF3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	32
Details	Motif: {"description":"Switch 2","evidences":[{"source":"PubMed","id":"30905672","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6IF2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6IF3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"30905672","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6IF2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6IF3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"30905672","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6IF2","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine; by LRRK2","evidences":[{"source":"PubMed","id":"29125462","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"O-(2-cholinephosphoryl)serine","evidences":[{"source":"PubMed","id":"21822290","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"22307087","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"O-AMP-tyrosine","evidences":[{"source":"PubMed","id":"21822290","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---