Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6G31

Crystal structure of human geranylgeranyl diphosphate synthase mutant D188Y bound to zoledronate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004161	molecular_function	dimethylallyltranstransferase activity
A	0004311	molecular_function	farnesyltranstransferase activity
A	0004337	molecular_function	geranyltranstransferase activity
A	0004659	molecular_function	prenyltransferase activity
A	0005515	molecular_function	protein binding
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006720	biological_process	isoprenoid metabolic process
A	0008299	biological_process	isoprenoid biosynthetic process
A	0016740	molecular_function	transferase activity
A	0030018	cellular_component	Z disc
A	0033384	biological_process	geranyl diphosphate biosynthetic process
A	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
A	0042802	molecular_function	identical protein binding
A	0045337	biological_process	farnesyl diphosphate biosynthetic process
A	0046872	molecular_function	metal ion binding
A	0048471	cellular_component	perinuclear region of cytoplasm
B	0004161	molecular_function	dimethylallyltranstransferase activity
B	0004311	molecular_function	farnesyltranstransferase activity
B	0004337	molecular_function	geranyltranstransferase activity
B	0004659	molecular_function	prenyltransferase activity
B	0005515	molecular_function	protein binding
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006720	biological_process	isoprenoid metabolic process
B	0008299	biological_process	isoprenoid biosynthetic process
B	0016740	molecular_function	transferase activity
B	0030018	cellular_component	Z disc
B	0033384	biological_process	geranyl diphosphate biosynthetic process
B	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
B	0042802	molecular_function	identical protein binding
B	0045337	biological_process	farnesyl diphosphate biosynthetic process
B	0046872	molecular_function	metal ion binding
B	0048471	cellular_component	perinuclear region of cytoplasm
C	0004161	molecular_function	dimethylallyltranstransferase activity
C	0004311	molecular_function	farnesyltranstransferase activity
C	0004337	molecular_function	geranyltranstransferase activity
C	0004659	molecular_function	prenyltransferase activity
C	0005515	molecular_function	protein binding
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006720	biological_process	isoprenoid metabolic process
C	0008299	biological_process	isoprenoid biosynthetic process
C	0016740	molecular_function	transferase activity
C	0030018	cellular_component	Z disc
C	0033384	biological_process	geranyl diphosphate biosynthetic process
C	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
C	0042802	molecular_function	identical protein binding
C	0045337	biological_process	farnesyl diphosphate biosynthetic process
C	0046872	molecular_function	metal ion binding
C	0048471	cellular_component	perinuclear region of cytoplasm
D	0004161	molecular_function	dimethylallyltranstransferase activity
D	0004311	molecular_function	farnesyltranstransferase activity
D	0004337	molecular_function	geranyltranstransferase activity
D	0004659	molecular_function	prenyltransferase activity
D	0005515	molecular_function	protein binding
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006720	biological_process	isoprenoid metabolic process
D	0008299	biological_process	isoprenoid biosynthetic process
D	0016740	molecular_function	transferase activity
D	0030018	cellular_component	Z disc
D	0033384	biological_process	geranyl diphosphate biosynthetic process
D	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
D	0042802	molecular_function	identical protein binding
D	0045337	biological_process	farnesyl diphosphate biosynthetic process
D	0046872	molecular_function	metal ion binding
D	0048471	cellular_component	perinuclear region of cytoplasm
E	0004161	molecular_function	dimethylallyltranstransferase activity
E	0004311	molecular_function	farnesyltranstransferase activity
E	0004337	molecular_function	geranyltranstransferase activity
E	0004659	molecular_function	prenyltransferase activity
E	0005515	molecular_function	protein binding
E	0005654	cellular_component	nucleoplasm
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006720	biological_process	isoprenoid metabolic process
E	0008299	biological_process	isoprenoid biosynthetic process
E	0016740	molecular_function	transferase activity
E	0030018	cellular_component	Z disc
E	0033384	biological_process	geranyl diphosphate biosynthetic process
E	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
E	0042802	molecular_function	identical protein binding
E	0045337	biological_process	farnesyl diphosphate biosynthetic process
E	0046872	molecular_function	metal ion binding
E	0048471	cellular_component	perinuclear region of cytoplasm
F	0004161	molecular_function	dimethylallyltranstransferase activity
F	0004311	molecular_function	farnesyltranstransferase activity
F	0004337	molecular_function	geranyltranstransferase activity
F	0004659	molecular_function	prenyltransferase activity
F	0005515	molecular_function	protein binding
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006720	biological_process	isoprenoid metabolic process
F	0008299	biological_process	isoprenoid biosynthetic process
F	0016740	molecular_function	transferase activity
F	0030018	cellular_component	Z disc
F	0033384	biological_process	geranyl diphosphate biosynthetic process
F	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
F	0042802	molecular_function	identical protein binding
F	0045337	biological_process	farnesyl diphosphate biosynthetic process
F	0046872	molecular_function	metal ion binding
F	0048471	cellular_component	perinuclear region of cytoplasm
G	0004161	molecular_function	dimethylallyltranstransferase activity
G	0004311	molecular_function	farnesyltranstransferase activity
G	0004337	molecular_function	geranyltranstransferase activity
G	0004659	molecular_function	prenyltransferase activity
G	0005515	molecular_function	protein binding
G	0005654	cellular_component	nucleoplasm
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0006720	biological_process	isoprenoid metabolic process
G	0008299	biological_process	isoprenoid biosynthetic process
G	0016740	molecular_function	transferase activity
G	0030018	cellular_component	Z disc
G	0033384	biological_process	geranyl diphosphate biosynthetic process
G	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
G	0042802	molecular_function	identical protein binding
G	0045337	biological_process	farnesyl diphosphate biosynthetic process
G	0046872	molecular_function	metal ion binding
G	0048471	cellular_component	perinuclear region of cytoplasm
H	0004161	molecular_function	dimethylallyltranstransferase activity
H	0004311	molecular_function	farnesyltranstransferase activity
H	0004337	molecular_function	geranyltranstransferase activity
H	0004659	molecular_function	prenyltransferase activity
H	0005515	molecular_function	protein binding
H	0005654	cellular_component	nucleoplasm
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0006720	biological_process	isoprenoid metabolic process
H	0008299	biological_process	isoprenoid biosynthetic process
H	0016740	molecular_function	transferase activity
H	0030018	cellular_component	Z disc
H	0033384	biological_process	geranyl diphosphate biosynthetic process
H	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
H	0042802	molecular_function	identical protein binding
H	0045337	biological_process	farnesyl diphosphate biosynthetic process
H	0046872	molecular_function	metal ion binding
H	0048471	cellular_component	perinuclear region of cytoplasm
I	0004161	molecular_function	dimethylallyltranstransferase activity
I	0004311	molecular_function	farnesyltranstransferase activity
I	0004337	molecular_function	geranyltranstransferase activity
I	0004659	molecular_function	prenyltransferase activity
I	0005515	molecular_function	protein binding
I	0005654	cellular_component	nucleoplasm
I	0005737	cellular_component	cytoplasm
I	0005829	cellular_component	cytosol
I	0006720	biological_process	isoprenoid metabolic process
I	0008299	biological_process	isoprenoid biosynthetic process
I	0016740	molecular_function	transferase activity
I	0030018	cellular_component	Z disc
I	0033384	biological_process	geranyl diphosphate biosynthetic process
I	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
I	0042802	molecular_function	identical protein binding
I	0045337	biological_process	farnesyl diphosphate biosynthetic process
I	0046872	molecular_function	metal ion binding
I	0048471	cellular_component	perinuclear region of cytoplasm
J	0004161	molecular_function	dimethylallyltranstransferase activity
J	0004311	molecular_function	farnesyltranstransferase activity
J	0004337	molecular_function	geranyltranstransferase activity
J	0004659	molecular_function	prenyltransferase activity
J	0005515	molecular_function	protein binding
J	0005654	cellular_component	nucleoplasm
J	0005737	cellular_component	cytoplasm
J	0005829	cellular_component	cytosol
J	0006720	biological_process	isoprenoid metabolic process
J	0008299	biological_process	isoprenoid biosynthetic process
J	0016740	molecular_function	transferase activity
J	0030018	cellular_component	Z disc
J	0033384	biological_process	geranyl diphosphate biosynthetic process
J	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
J	0042802	molecular_function	identical protein binding
J	0045337	biological_process	farnesyl diphosphate biosynthetic process
J	0046872	molecular_function	metal ion binding
J	0048471	cellular_component	perinuclear region of cytoplasm
K	0004161	molecular_function	dimethylallyltranstransferase activity
K	0004311	molecular_function	farnesyltranstransferase activity
K	0004337	molecular_function	geranyltranstransferase activity
K	0004659	molecular_function	prenyltransferase activity
K	0005515	molecular_function	protein binding
K	0005654	cellular_component	nucleoplasm
K	0005737	cellular_component	cytoplasm
K	0005829	cellular_component	cytosol
K	0006720	biological_process	isoprenoid metabolic process
K	0008299	biological_process	isoprenoid biosynthetic process
K	0016740	molecular_function	transferase activity
K	0030018	cellular_component	Z disc
K	0033384	biological_process	geranyl diphosphate biosynthetic process
K	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
K	0042802	molecular_function	identical protein binding
K	0045337	biological_process	farnesyl diphosphate biosynthetic process
K	0046872	molecular_function	metal ion binding
K	0048471	cellular_component	perinuclear region of cytoplasm
L	0004161	molecular_function	dimethylallyltranstransferase activity
L	0004311	molecular_function	farnesyltranstransferase activity
L	0004337	molecular_function	geranyltranstransferase activity
L	0004659	molecular_function	prenyltransferase activity
L	0005515	molecular_function	protein binding
L	0005654	cellular_component	nucleoplasm
L	0005737	cellular_component	cytoplasm
L	0005829	cellular_component	cytosol
L	0006720	biological_process	isoprenoid metabolic process
L	0008299	biological_process	isoprenoid biosynthetic process
L	0016740	molecular_function	transferase activity
L	0030018	cellular_component	Z disc
L	0033384	biological_process	geranyl diphosphate biosynthetic process
L	0033386	biological_process	geranylgeranyl diphosphate biosynthetic process
L	0042802	molecular_function	identical protein binding
L	0045337	biological_process	farnesyl diphosphate biosynthetic process
L	0046872	molecular_function	metal ion binding
L	0048471	cellular_component	perinuclear region of cytoplasm

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	binding site for residue ZOL A 401

Chain	Residue
A	ASP64
A	MG404
A	ASP68
A	ARG73
A	GLN126
A	LYS151
A	GLN185
A	LYS212
A	MG402
A	MG403

site_id	AC2
Number of Residues	2
Details	binding site for residue MG A 402

Chain	Residue
A	GLN185
A	ZOL401

site_id	AC3
Number of Residues	3
Details	binding site for residue MG A 403

Chain	Residue
A	ASP64
A	ASP68
A	ZOL401

site_id	AC4
Number of Residues	4
Details	binding site for residue MG A 404

Chain	Residue
A	ASP64
A	ASP68
A	GLN126
A	ZOL401

site_id	AC5
Number of Residues	7
Details	binding site for residue ZOL B 401

Chain	Residue
B	ASP64
B	ASP68
B	ARG73
B	GLN185
B	MG402
B	MG403
B	MG404

site_id	AC6
Number of Residues	1
Details	binding site for residue MG B 402

Chain	Residue
B	ZOL401

site_id	AC7
Number of Residues	3
Details	binding site for residue MG B 403

Chain	Residue
B	ASP64
B	ASP68
B	ZOL401

site_id	AC8
Number of Residues	3
Details	binding site for residue MG B 404

Chain	Residue
B	ASP64
B	ASP68
B	ZOL401

site_id	AC9
Number of Residues	8
Details	binding site for residue ZOL C 401

Chain	Residue
C	ASP64
C	ASP68
C	ARG73
C	GLN126
C	LYS151
C	MG402
C	MG403
C	MG404

site_id	AD1
Number of Residues	2
Details	binding site for residue MG C 402

Chain	Residue
C	ASP189
C	ZOL401

site_id	AD2
Number of Residues	4
Details	binding site for residue MG C 403

Chain	Residue
C	ASP64
C	ASP68
C	ARG73
C	ZOL401

site_id	AD3
Number of Residues	5
Details	binding site for residue MG C 404

Chain	Residue
C	ASP64
C	ASP68
C	GLN126
C	ASP129
C	ZOL401

site_id	AD4
Number of Residues	7
Details	binding site for residue ZOL D 401

Chain	Residue
D	ASP64
D	ASP68
D	ARG73
D	GLN126
D	MG402
D	MG403
D	MG404

site_id	AD5
Number of Residues	1
Details	binding site for residue MG D 402

Chain	Residue
D	ZOL401

site_id	AD6
Number of Residues	5
Details	binding site for residue MG D 403

Chain	Residue
D	ASP64
D	ASP68
D	ARG73
D	ZOL401
D	MG404

site_id	AD7
Number of Residues	5
Details	binding site for residue MG D 404

Chain	Residue
D	ASP64
D	ASP68
D	GLN126
D	ZOL401
D	MG403

site_id	AD8
Number of Residues	6
Details	binding site for residue ZOL E 401

Chain	Residue
E	ASP64
E	ASP68
E	ARG73
E	MG402
E	MG403
E	MG404

site_id	AD9
Number of Residues	2
Details	binding site for residue MG E 402

Chain	Residue
E	TYR188
E	ZOL401

site_id	AE1
Number of Residues	4
Details	binding site for residue MG E 403

Chain	Residue
E	ASP64
E	ASP68
E	ZOL401
E	MG404

site_id	AE2
Number of Residues	4
Details	binding site for residue MG E 404

Chain	Residue
E	ASP64
E	ASP68
E	ZOL401
E	MG403

site_id	AE3
Number of Residues	7
Details	binding site for residue ZOL F 401

Chain	Residue
F	ASP64
F	ASP68
F	ARG73
F	GLN126
F	MG402
F	MG403
F	MG404

site_id	AE4
Number of Residues	2
Details	binding site for residue MG F 402

Chain	Residue
F	ASP189
F	ZOL401

site_id	AE5
Number of Residues	3
Details	binding site for residue MG F 403

Chain	Residue
F	ASP64
F	ASP68
F	ZOL401

site_id	AE6
Number of Residues	4
Details	binding site for residue MG F 404

Chain	Residue
F	ASP68
F	ASP129
F	ZOL401
F	ASP64

site_id	AE7
Number of Residues	9
Details	binding site for residue ZOL G 401

Chain	Residue
G	ASP64
G	ASP68
G	ARG73
G	GLN126
G	LYS151
G	TYR188
G	MG402
G	MG403
G	MG404

site_id	AE8
Number of Residues	1
Details	binding site for residue MG G 402

Chain	Residue
G	ZOL401

site_id	AE9
Number of Residues	4
Details	binding site for residue MG G 403

Chain	Residue
G	ASP64
G	ASP68
G	ZOL401
G	MG404

site_id	AF1
Number of Residues	4
Details	binding site for residue MG G 404

Chain	Residue
G	ASP64
G	ASP68
G	ZOL401
G	MG403

site_id	AF2
Number of Residues	7
Details	binding site for residue ZOL H 401

Chain	Residue
H	ASP64
H	ASP68
H	GLN185
H	LYS212
H	MG402
H	MG403
H	MG404

site_id	AF3
Number of Residues	2
Details	binding site for residue MG H 402

Chain	Residue
H	TYR188
H	ZOL401

site_id	AF4
Number of Residues	3
Details	binding site for residue MG H 403

Chain	Residue
H	ASP64
H	ASP68
H	ZOL401

site_id	AF5
Number of Residues	5
Details	binding site for residue MG H 404

Chain	Residue
H	ASP64
H	ASP68
H	GLN126
H	ASP129
H	ZOL401

site_id	AF6
Number of Residues	7
Details	binding site for residue ZOL I 401

Chain	Residue
I	ASP64
I	ASP68
I	LYS151
I	GLN185
I	MG402
I	MG403
I	MG404

site_id	AF7
Number of Residues	2
Details	binding site for residue MG I 402

Chain	Residue
I	TYR188
I	ZOL401

site_id	AF8
Number of Residues	3
Details	binding site for residue MG I 403

Chain	Residue
I	ASP64
I	ASP68
I	ZOL401

site_id	AF9
Number of Residues	3
Details	binding site for residue MG I 404

Chain	Residue
I	ASP64
I	ASP68
I	ZOL401

site_id	AG1
Number of Residues	7
Details	binding site for residue ZOL J 401

Chain	Residue
J	ASP64
J	ASP68
J	ARG73
J	GLN185
J	MG402
J	MG403
J	MG404

site_id	AG2
Number of Residues	1
Details	binding site for residue MG J 402

Chain	Residue
J	ZOL401

site_id	AG3
Number of Residues	5
Details	binding site for residue MG J 403

Chain	Residue
J	ASP64
J	ASP68
J	GLU210
J	ZOL401
J	MG404

site_id	AG4
Number of Residues	6
Details	binding site for residue MG J 404

Chain	Residue
J	ASP64
J	ASP68
J	GLN126
J	ASP129
J	ZOL401
J	MG403

site_id	AG5
Number of Residues	7
Details	binding site for residue ZOL K 401

Chain	Residue
K	ASP64
K	ASP68
K	ARG73
K	GLN126
K	MG402
K	MG403
K	MG404

site_id	AG6
Number of Residues	3
Details	binding site for residue MG K 402

Chain	Residue
K	ASN192
K	ASP207
K	ZOL401

site_id	AG7
Number of Residues	4
Details	binding site for residue MG K 403

Chain	Residue
K	ASP64
K	ASP68
K	SER70
K	ZOL401

site_id	AG8
Number of Residues	5
Details	binding site for residue MG K 404

Chain	Residue
K	ASP64
K	ASP68
K	GLN126
K	ASP129
K	ZOL401

site_id	AG9
Number of Residues	7
Details	binding site for residue ZOL L 401

Chain	Residue
L	ASP64
L	ASP68
L	GLN126
L	LYS212
L	MG402
L	MG403
L	MG404

site_id	AH1
Number of Residues	1
Details	binding site for residue MG L 402

Chain	Residue
L	ZOL401

site_id	AH2
Number of Residues	3
Details	binding site for residue MG L 403

Chain	Residue
L	ASP64
L	ASP68
L	ZOL401

site_id	AH3
Number of Residues	5
Details	binding site for residue MG L 404

Chain	Residue
L	ASP64
L	ASP68
L	ASP129
L	LYS212
L	ZOL401

Functional Information from PROSITE/UniProt

site_id	PS00723
Number of Residues	15
Details	POLYPRENYL_SYNTHASE_1 Polyprenyl synthases signature 1. LLiDDie..DnsklRRG

Chain	Residue	Details
A	LEU61-GLY75

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	36
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P14324

Chain	Residue	Details
A	LYS25
D	LYS25
D	ARG28
D	ARG74
E	LYS25
E	ARG28
E	ARG74
F	LYS25
F	ARG28
F	ARG74
G	LYS25
A	ARG28
G	ARG28
G	ARG74
H	LYS25
H	ARG28
H	ARG74
I	LYS25
I	ARG28
I	ARG74
J	LYS25
J	ARG28
A	ARG74
J	ARG74
K	LYS25
K	ARG28
K	ARG74
L	LYS25
L	ARG28
L	ARG74
B	LYS25
B	ARG28
B	ARG74
C	LYS25
C	ARG28
C	ARG74

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:Q12051

Chain	Residue	Details
A	HIS57
J	HIS57
K	HIS57
L	HIS57
B	HIS57
C	HIS57
D	HIS57
E	HIS57
F	HIS57
G	HIS57
H	HIS57
I	HIS57

site_id	SWS_FT_FI3
Number of Residues	24
Details	BINDING: BINDING => ECO:0000269\|PubMed:16698791

Chain	Residue	Details
A	ASP64
E	ASP68
F	ASP64
F	ASP68
G	ASP64
G	ASP68
H	ASP64
H	ASP68
I	ASP64
I	ASP68
J	ASP64
A	ASP68
J	ASP68
K	ASP64
K	ASP68
L	ASP64
L	ASP68
B	ASP64
B	ASP68
C	ASP64
C	ASP68
D	ASP64
D	ASP68
E	ASP64

site_id	SWS_FT_FI4
Number of Residues	60
Details	BINDING:

Chain	Residue	Details
A	ARG73
B	LYS202
C	ARG73
C	LYS151
C	THR152
C	GLN185
C	LYS202
D	ARG73
D	LYS151
D	THR152
D	GLN185
A	LYS151
D	LYS202
E	ARG73
E	LYS151
E	THR152
E	GLN185
E	LYS202
F	ARG73
F	LYS151
F	THR152
F	GLN185
A	THR152
F	LYS202
G	ARG73
G	LYS151
G	THR152
G	GLN185
G	LYS202
H	ARG73
H	LYS151
H	THR152
H	GLN185
A	GLN185
H	LYS202
I	ARG73
I	LYS151
I	THR152
I	GLN185
I	LYS202
J	ARG73
J	LYS151
J	THR152
J	GLN185
A	LYS202
J	LYS202
K	ARG73
K	LYS151
K	THR152
K	GLN185
K	LYS202
L	ARG73
L	LYS151
L	THR152
L	GLN185
B	ARG73
L	LYS202
B	LYS151
B	THR152
B	GLN185

site_id	SWS_FT_FI5
Number of Residues	12
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	LYS212
J	LYS212
K	LYS212
L	LYS212
B	LYS212
C	LYS212
D	LYS212
E	LYS212
F	LYS212
G	LYS212
H	LYS212
I	LYS212

site_id	SWS_FT_FI6
Number of Residues	12
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:22814378

Chain	Residue	Details
A	MET1
J	MET1
K	MET1
L	MET1
B	MET1
C	MET1
D	MET1
E	MET1
F	MET1
G	MET1
H	MET1
I	MET1

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