Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6R4V

Crystal structure of human geranylgeranyl diphosphate synthase bound to ibandronate

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue MG A 1301

Chain	Residue
A	ASP64
A	ASP68
A	MG1303
A	BFQ1304
A	HOH1422
A	HOH1427

site_id	AC2
Number of Residues	6
Details	binding site for residue MG A 1302

Chain	Residue
A	BFQ1304
A	HOH1411
A	HOH1519
A	GLN185
A	ASP188
A	ASN192

site_id	AC3
Number of Residues	7
Details	binding site for residue MG A 1303

Chain	Residue
A	ASP64
A	ASP68
A	MG1301
A	BFQ1304
A	HOH1405
A	HOH1418
A	HOH1423

site_id	AC4
Number of Residues	19
Details	binding site for residue BFQ A 1304

Chain	Residue
A	SER60
A	ASP64
A	ASP68
A	ARG73
A	GLN126
A	LYS151
A	GLN185
A	ASP188
A	LYS202
A	LYS212
A	MG1301
A	MG1302
A	MG1303
A	HOH1405
A	HOH1418
A	HOH1422
A	HOH1427
A	HOH1519
A	HOH1555

site_id	AC5
Number of Residues	4
Details	binding site for residue GOL A 1305

Chain	Residue
A	LYS25
A	ARG28
A	HIS57
A	PHE184

site_id	AC6
Number of Residues	6
Details	binding site for residue MG C 1301

Chain	Residue
C	ASP64
C	ASP68
C	MG1302
C	BFQ1303
C	HOH1439
C	HOH1479

site_id	AC7
Number of Residues	7
Details	binding site for residue MG C 1302

Chain	Residue
C	ASP64
C	ASP68
C	MG1301
C	BFQ1303
C	HOH1419
C	HOH1431
C	HOH1467

site_id	AC8
Number of Residues	6
Details	binding site for residue GOL C 1304

Chain	Residue
C	GLY24
C	LYS25
C	HIS57
C	ARG74
C	PHE184
C	HOH1432

site_id	AC9
Number of Residues	6
Details	binding site for residue MG F 1301

Chain	Residue
F	ASP64
F	ASP68
F	MG1303
F	BFQ1304
F	HOH1412
F	HOH1413

site_id	AD1
Number of Residues	5
Details	binding site for residue MG F 1302

Chain	Residue
F	ASP207
F	LYS212
F	BFQ1304
F	HOH1430
F	HOH1520

site_id	AD2
Number of Residues	7
Details	binding site for residue MG F 1303

Chain	Residue
F	ASP64
F	ASP68
F	MG1301
F	BFQ1304
F	HOH1417
F	HOH1429
F	HOH1460

site_id	AD3
Number of Residues	18
Details	binding site for residue BFQ F 1304

Chain	Residue
F	SER60
F	ASP64
F	ASP68
F	ARG73
F	LEU122
F	GLN126
F	LYS151
F	GLN185
F	LYS202
F	LYS212
F	MG1301
F	MG1302
F	MG1303
F	HOH1412
F	HOH1413
F	HOH1416
F	HOH1429
F	HOH1460

site_id	AD4
Number of Residues	7
Details	binding site for residue MG E 1301

Chain	Residue
E	LYS202
E	MG1303
E	BFQ1304
E	HOH1408
E	HOH1463
E	ASP64
E	ASP68

site_id	AD5
Number of Residues	5
Details	binding site for residue MG E 1302

Chain	Residue
E	ASP188
E	BFQ1304
E	HOH1405
E	HOH1425
E	HOH1509

site_id	AD6
Number of Residues	7
Details	binding site for residue MG E 1303

Chain	Residue
E	ASP64
E	ASP68
E	MG1301
E	BFQ1304
E	HOH1409
E	HOH1462
E	HOH1469

site_id	AD7
Number of Residues	16
Details	binding site for residue BFQ E 1304

Chain	Residue
E	ASP64
E	ASP68
E	ARG73
E	LYS151
E	GLN185
E	ASP188
E	LYS202
E	LYS212
E	MG1301
E	MG1302
E	MG1303
E	HOH1405
E	HOH1409
E	HOH1462
E	HOH1463
E	HOH1480

site_id	AD8
Number of Residues	6
Details	binding site for residue MG B 1301

Chain	Residue
B	ASP64
B	ASP68
B	MG1303
B	BFQ1304
B	HOH1430
B	HOH1447

site_id	AD9
Number of Residues	4
Details	binding site for residue MG B 1302

Chain	Residue
B	ASP188
B	BFQ1304
B	HOH1416
B	HOH1418

site_id	AE1
Number of Residues	7
Details	binding site for residue MG B 1303

Chain	Residue
B	ASP64
B	ASP68
B	MG1301
B	BFQ1304
B	HOH1406
B	HOH1421
B	HOH1455

site_id	AE2
Number of Residues	17
Details	binding site for residue BFQ B 1304

Chain	Residue
B	SER60
B	ASP64
B	ASP68
B	ARG73
B	LEU122
B	GLN126
B	LYS151
B	GLN185
B	ASP188
B	LYS212
B	MG1301
B	MG1302
B	MG1303
B	HOH1406
B	HOH1416
B	HOH1430
B	HOH1455

site_id	AE3
Number of Residues	6
Details	binding site for residue MG D 1301

Chain	Residue
D	ASP64
D	ASP68
D	MG1303
D	BFQ1304
D	HOH1443
D	HOH1455

site_id	AE4
Number of Residues	5
Details	binding site for residue MG D 1302

Chain	Residue
D	ASP188
D	BFQ1304
D	HOH1406
D	HOH1423
D	HOH1434

site_id	AE5
Number of Residues	7
Details	binding site for residue MG D 1303

Chain	Residue
D	ASP64
D	ASP68
D	MG1301
D	BFQ1304
D	HOH1403
D	HOH1414
D	HOH1450

site_id	AE6
Number of Residues	18
Details	binding site for residue BFQ D 1304

Chain	Residue
D	SER60
D	ASP64
D	ASP68
D	ARG73
D	GLN126
D	LYS151
D	GLN185
D	ASP188
D	LYS212
D	MG1301
D	MG1302
D	MG1303
D	HOH1403
D	HOH1434
D	HOH1443
D	HOH1450
D	HOH1455
D	HOH1495

site_id	AE7
Number of Residues	24
Details	binding site for Di-peptide BFQ C 1303 and LYS C 151

Chain	Residue
C	SER60
C	ASP64
C	ASP68
C	ARG73
C	LEU122
C	GLN126
C	ASP129
C	MET147
C	VAL148
C	LEU149
C	GLN150
C	THR152
C	GLN185
C	ASP188
C	LYS202
C	LYS212
C	MG1301
C	MG1302
C	HOH1403
C	HOH1408
C	HOH1426
C	HOH1431
C	HOH1439
C	HOH1467

Functional Information from PROSITE/UniProt

site_id	PS00444
Number of Residues	13
Details	POLYPRENYL_SYNTHASE_2 Polyprenyl synthases signature 2. LGlfFQIrDDYaN

Chain	Residue	Details
A	LEU180-ASN192

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	18
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:P14324

Chain	Residue	Details
A	LYS25
E	LYS25
E	ARG28
E	ARG74
B	LYS25
B	ARG28
B	ARG74
D	LYS25
D	ARG28
D	ARG74
A	ARG28
A	ARG74
C	LYS25
C	ARG28
C	ARG74
F	LYS25
F	ARG28
F	ARG74

site_id	SWS_FT_FI2
Number of Residues	6
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:Q12051

Chain	Residue	Details
A	HIS57
C	HIS57
F	HIS57
E	HIS57
B	HIS57
D	HIS57

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:16698791

Chain	Residue	Details
A	ASP64
B	ASP68
D	ASP64
D	ASP68
A	ASP68
C	ASP64
C	ASP68
F	ASP64
F	ASP68
E	ASP64
E	ASP68
B	ASP64

site_id	SWS_FT_FI4
Number of Residues	30
Details	BINDING:

Chain	Residue	Details
A	ARG73
C	LYS202
F	ARG73
F	LYS151
F	THR152
F	GLN185
F	LYS202
E	ARG73
E	LYS151
E	THR152
E	GLN185
A	LYS151
E	LYS202
B	ARG73
B	LYS151
B	THR152
B	GLN185
B	LYS202
D	ARG73
D	LYS151
D	THR152
D	GLN185
A	THR152
D	LYS202
A	GLN185
A	LYS202
C	ARG73
C	LYS151
C	THR152
C	GLN185

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	LYS212
C	LYS212
F	LYS212
E	LYS212
B	LYS212
D	LYS212

site_id	SWS_FT_FI6
Number of Residues	6
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:22814378

Chain	Residue	Details
A	MET1
C	MET1
F	MET1
E	MET1
B	MET1
D	MET1

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