Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3EBL

Crystal Structure of Rice GID1 complexed with GA4

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0009739	biological_process	response to gibberellin
A	0009740	biological_process	gibberellic acid mediated signaling pathway
A	0009939	biological_process	positive regulation of gibberellic acid mediated signaling pathway
A	0010325	biological_process	raffinose family oligosaccharide biosynthetic process
A	0010331	molecular_function	gibberellin binding
A	0016787	molecular_function	hydrolase activity
A	0048444	biological_process	floral organ morphogenesis
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0009739	biological_process	response to gibberellin
B	0009740	biological_process	gibberellic acid mediated signaling pathway
B	0009939	biological_process	positive regulation of gibberellic acid mediated signaling pathway
B	0010325	biological_process	raffinose family oligosaccharide biosynthetic process
B	0010331	molecular_function	gibberellin binding
B	0016787	molecular_function	hydrolase activity
B	0048444	biological_process	floral organ morphogenesis
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0009739	biological_process	response to gibberellin
C	0009740	biological_process	gibberellic acid mediated signaling pathway
C	0009939	biological_process	positive regulation of gibberellic acid mediated signaling pathway
C	0010325	biological_process	raffinose family oligosaccharide biosynthetic process
C	0010331	molecular_function	gibberellin binding
C	0016787	molecular_function	hydrolase activity
C	0048444	biological_process	floral organ morphogenesis
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0009739	biological_process	response to gibberellin
D	0009740	biological_process	gibberellic acid mediated signaling pathway
D	0009939	biological_process	positive regulation of gibberellic acid mediated signaling pathway
D	0010325	biological_process	raffinose family oligosaccharide biosynthetic process
D	0010331	molecular_function	gibberellin binding
D	0016787	molecular_function	hydrolase activity
D	0048444	biological_process	floral organ morphogenesis
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0009739	biological_process	response to gibberellin
E	0009740	biological_process	gibberellic acid mediated signaling pathway
E	0009939	biological_process	positive regulation of gibberellic acid mediated signaling pathway
E	0010325	biological_process	raffinose family oligosaccharide biosynthetic process
E	0010331	molecular_function	gibberellin binding
E	0016787	molecular_function	hydrolase activity
E	0048444	biological_process	floral organ morphogenesis
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0009739	biological_process	response to gibberellin
F	0009740	biological_process	gibberellic acid mediated signaling pathway
F	0009939	biological_process	positive regulation of gibberellic acid mediated signaling pathway
F	0010325	biological_process	raffinose family oligosaccharide biosynthetic process
F	0010331	molecular_function	gibberellin binding
F	0016787	molecular_function	hydrolase activity
F	0048444	biological_process	floral organ morphogenesis

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GA4 A 401

Chain	Residue
A	ILE24
A	ARG251
A	TYR254
A	VAL326
A	GLY327
A	TYR329
A	HOH605
A	HOH607
A	PHE27
A	GLY122
A	SER123
A	ILE133
A	TYR134
A	ASP197
A	SER198
A	VAL246

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD A 501

Chain	Residue
A	LEU23
A	LEU49
A	ASP50
A	ARG51
A	HOH640
B	MPD501

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NO3 A 601

Chain	Residue
A	ARG35
A	HOH785
A	HOH848

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 A 602

Chain	Residue
A	THR231
A	ASP264
A	ARG265
A	HOH698

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NO3 A 603

Chain	Residue
A	ARG51
A	LEU331
A	NO3604

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NO3 A 604

Chain	Residue
A	HIS19
A	LEU23
A	ARG51
A	NO3603
B	ASN26
B	SER30

site_id	AC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GA4 B 401

Chain	Residue
B	ILE24
B	PHE27
B	GLY122
B	SER123
B	ILE133
B	TYR134
B	ASP197
B	SER198
B	ARG251
B	TYR254
B	VAL326
B	GLY327
B	TYR329
B	HOH702

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD B 501

Chain	Residue
A	MPD501
B	LEU23
B	SER30
B	LEU49
B	ARG51
B	HOH719

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NO3 B 601

Chain	Residue
B	ARG35
B	TRP253
B	HOH891

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 B 602

Chain	Residue
B	THR231
B	ASP264
B	ARG265
B	HOH789

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NO3 B 604

Chain	Residue
A	ASN26
A	SER30
B	HIS19
B	LEU23
B	ARG51
B	PO4701

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 B 701

Chain	Residue
B	ARG51
B	LEU330
B	LEU331
B	NO3604
B	HOH724

site_id	BC4
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GA4 C 401

Chain	Residue
C	PHE27
C	ARG35
C	GLY122
C	SER123
C	ILE133
C	TYR134
C	ASP197
C	SER198
C	VAL246
C	ARG251
C	TYR254
C	VAL326
C	GLY327
C	TYR329
C	HOH605
C	HOH607

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MPD C 501

Chain	Residue
D	ARG51
C	ASN26
C	SER30
C	LEU49
C	ASP50
C	ARG51
C	HOH638
D	ASN26

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NO3 C 601

Chain	Residue
C	ARG35
C	TRP253

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 C 602

Chain	Residue
C	THR231
C	ASP264
C	ARG265
C	HOH697

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NO3 C 603

Chain	Residue
C	ARG51
C	LEU330
C	HOH642

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NO3 C 604

Chain	Residue
C	ASN26
C	SER30
D	HIS19
D	LEU23
D	ARG51

site_id	CC1
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GA4 D 401

Chain	Residue
D	ILE24
D	PHE27
D	ARG35
D	GLY122
D	SER123
D	ILE133
D	TYR134
D	ASP197
D	SER198
D	ARG251
D	TYR254
D	VAL326
D	GLY327
D	TYR329
D	HOH604
D	HOH606

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD D 501

Chain	Residue
D	LEU23
D	ASN26
D	LEU49
D	ASP50
D	ARG51
D	HOH630

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 D 601

Chain	Residue
D	ARG35
D	GLN249
D	TRP253
D	HOH704

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 D 602

Chain	Residue
D	THR231
D	ASP264
D	ARG265
D	HOH721

site_id	CC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NO3 D 603

Chain	Residue
D	ARG51
D	LEU331

site_id	CC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE PO4 E 701

Chain	Residue
E	ARG51
E	SER136
E	LEU330

site_id	CC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GA4 E 401

Chain	Residue
E	PHE27
E	ARG35
E	GLY122
E	SER123
E	ILE133
E	TYR134
E	ASP197
E	SER198
E	ARG251
E	TYR254
E	VAL326
E	GLY327
E	TYR329
E	HOH702
E	HOH730

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD E 501

Chain	Residue
E	ASN26
E	SER30
E	LEU49
E	ARG51
E	HOH711
F	MPD501

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE NO3 E 601

Chain	Residue
E	ARG35
E	GLN249
E	TRP253
E	HOH796

site_id	DC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GA4 F 401

Chain	Residue
F	PHE27
F	GLY122
F	SER123
F	ILE133
F	TYR134
F	ASP197
F	SER198
F	PHE245
F	ARG251
F	TYR254
F	VAL326
F	GLY327
F	TYR329
F	HOH604
F	HOH625

site_id	DC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MPD F 501

Chain	Residue
E	MPD501
F	LEU23
F	SER30
F	LEU49
F	ARG51
F	HOH626

site_id	DC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE NO3 F 601

Chain	Residue
F	ARG35
F	HOH752

site_id	DC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NO3 F 602

Chain	Residue
F	THR231
F	ASP264
F	ARG265

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NO3 F 603

Chain	Residue
F	LEU330
F	LEU331
F	HOH631

Functional Information from PROSITE/UniProt

site_id	PS01173
Number of Residues	17
Details	LIPASE_GDXG_HIS Lipolytic enzymes "G-D-X-G" family, putative histidine active site. IIfFHGGSFvhsSasST

Chain	Residue	Details
A	ILE116-THR132

site_id	PS01174
Number of Residues	13
Details	LIPASE_GDXG_SER Lipolytic enzymes "G-D-X-G" family, putative serine active site. VfLSGDSSGGnIA

Chain	Residue	Details
A	VAL192-ALA204

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Motif: {"description":"Involved in the stabilization of the negatively charged intermediate by the formation of the oxyanion hole","evidences":[{"source":"UniProtKB","id":"Q5NUF3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Active site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU10038","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Active site: {"evidences":[{"source":"UniProtKB","id":"Q5NUF3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19037316","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3EBL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19037316","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3ED1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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