Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4IRU

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0003924	molecular_function	GTPase activity
B	0005525	molecular_function	GTP binding
D	0003924	molecular_function	GTPase activity
D	0005525	molecular_function	GTP binding
F	0003924	molecular_function	GTPase activity
F	0005525	molecular_function	GTP binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT A 901

Chain	Residue
A	ASP599
A	LYS606

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT A 902

Chain	Residue
A	LEU367
A	LEU368
A	K910

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 903

Chain	Residue
C	THR330
A	THR330
A	LEU332
C	PRO328
C	LEU329

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 904

Chain	Residue
A	ARG395
A	PRO400
A	TYR539
A	PRO540

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 905

Chain	Residue
A	LEU562
A	ASN563
A	SER564

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 906

Chain	Residue
A	HIS415
B	ASP92

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 907

Chain	Residue
A	HIS417
A	SER443
A	ARG444
A	ARG596
A	THR597
A	ASP598
A	HOH1006

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 908

Chain	Residue
A	SER564
A	PRO565
A	LYS566
A	PRO567
A	SER568

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K A 909

Chain	Residue
A	GLU536
A	ASN563

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K A 910

Chain	Residue
A	ASN363
A	ACT902

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE K A 911

Chain	Residue
A	SER564
A	PRO565
A	GLU609

site_id	BC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE K A 912

Chain	Residue
A	THR384

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 201

Chain	Residue
B	SER25
B	THR43
B	GDP202
B	AF3203
B	HOH302
B	HOH303

site_id	BC5
Number of Residues	22
Details	BINDING SITE FOR RESIDUE GDP B 202

Chain	Residue
A	ARG444
B	GLY21
B	VAL22
B	GLY23
B	LYS24
B	SER25
B	CYS26
B	TYR36
B	SER39
B	TYR40
B	ILE41
B	ASN124
B	LYS125
B	ASP127
B	LEU128
B	SER154
B	ALA155
B	LYS156
B	MG201
B	AF3203
B	HOH302
B	HOH303

site_id	BC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AF3 B 203

Chain	Residue
A	ARG444
B	ASP19
B	SER20
B	LYS24
B	SER42
B	THR43
B	GLY69
B	GLN70
B	MG201
B	GDP202
B	HOH302
B	HOH303
B	HOH308

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT B 204

Chain	Residue
B	SER79
B	ARG82
B	GOL206

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT B 205

Chain	Residue
B	ASP19
B	ARG74
B	GLN104

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 206

Chain	Residue
B	LYS13
B	GLN63
B	TRP65
B	TYR80
B	ARG82
B	ACT204

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE ACT C 701

Chain	Residue
C	HIS415
D	ASP92

site_id	CC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT C 702

Chain	Residue
C	ASP599
C	LYS606
C	ACT706

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT C 703

Chain	Residue
C	ARG444
C	ARG596
C	THR597
C	ASP598
C	HIS417
C	SER443

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACT C 704

Chain	Residue
C	ASN389
C	PRO524
C	PHE526
C	ALA527
C	GLU528

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACT C 705

Chain	Residue
C	ASN532
C	GLU534
C	SER535
C	TYR539
C	PRO540
C	ILE541

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE ACT C 706

Chain	Residue
C	LEU562
C	SER564
C	ACT702

site_id	CC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE K C 708

Chain	Residue
C	GLU536

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 201

Chain	Residue
D	SER25
D	THR43
D	GDP202
D	AF3203
D	HOH302
D	HOH303

site_id	CC9
Number of Residues	25
Details	BINDING SITE FOR RESIDUE GDP D 202

Chain	Residue
C	HIS415
C	ARG444
D	SER20
D	GLY21
D	VAL22
D	GLY23
D	LYS24
D	SER25
D	CYS26
D	TYR36
D	SER39
D	TYR40
D	ILE41
D	ASN124
D	LYS125
D	ASP127
D	LEU128
D	SER154
D	ALA155
D	LYS156
D	MG201
D	AF3203
D	ACT205
D	HOH302
D	HOH303

site_id	DC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AF3 D 203

Chain	Residue
C	ARG444
D	SER20
D	GLY21
D	LYS24
D	SER42
D	THR43
D	GLY69
D	GLN70
D	MG201
D	GDP202
D	HOH301
D	HOH302
D	HOH303

site_id	DC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT D 204

Chain	Residue
D	ASP19
D	GLU71
D	ARG74
D	GLN104

site_id	DC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE ACT D 205

Chain	Residue
D	GLU38
D	LEU128
D	LYS156
D	GDP202

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG F 200

Chain	Residue
F	LYS24
F	SER25
F	ASP66
F	GDP201
F	AF3202

site_id	DC5
Number of Residues	20
Details	BINDING SITE FOR RESIDUE GDP F 201

Chain	Residue
E	ARG444
F	ASP19
F	GLY21
F	VAL22
F	GLY23
F	LYS24
F	SER25
F	CYS26
F	TYR36
F	GLU38
F	TYR40
F	ILE41
F	ASN124
F	LYS125
F	LEU128
F	SER154
F	ALA155
F	LYS156
F	MG200
F	AF3202

site_id	DC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE AF3 F 202

Chain	Residue
F	ASP19
F	SER20
F	GLY21
F	LYS24
F	THR43
F	THR67
F	GLN70
F	MG200
F	GDP201

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. LLLiGDSGVGKscL

Chain	Residue	Details
B	LEU14-LEU27

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI2
Number of Residues	42
Details	Motif: {"description":"Switch 1","evidences":[{"source":"PubMed","id":"22416225","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3SFV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TKL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	51
Details	Motif: {"description":"Switch 2","evidences":[{"source":"PubMed","id":"22416225","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3SFV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TKL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	36
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22416225","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3TKL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22416225","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22939626","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23588383","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23821544","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of human RAB1A in complex with GDP.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"PDB","id":"2FOL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TKL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FME","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4IRU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4JVS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22416225","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22939626","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23588383","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23821544","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of human RAB1A in complex with GDP.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"PDB","id":"3TKL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FME","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4IRU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4JVS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22416225","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22939626","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23588383","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of human RAB1A in complex with GDP.","authoringGroup":["Structural genomics consortium (SGC)"]}},{"source":"PDB","id":"3TKL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FMD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FME","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4JVS","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	3
Details	Modified residue: {"description":"N-acetylserine","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"NOV-2005","submissionDatabase":"UniProtKB","authors":["Bienvenut W.V.","Claeys D."]}},{"source":"PubMed","id":"22223895","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	3
Details	Modified residue: {"description":"(Microbial infection) O-(2-cholinephosphoryl)serine","evidences":[{"source":"PubMed","id":"21822290","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22158903","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	3
Details	Glycosylation: {"description":"(Microbial infection) N-beta-linked (GlcNAc) arginine","evidences":[{"source":"PubMed","id":"32504010","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	9
Details	Glycosylation: {"description":"(Microbial infection) N-beta-linked (GlcNAc) arginine","evidences":[{"source":"PubMed","id":"32504010","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32974215","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	9
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P51153","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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