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3VC1

Crystal structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor A3(2) in complex with Mg2+, geranyl-S-thiolodiphosphate, and S-adenosyl-L-homocysteine

Functional Information from GO Data
ChainGOidnamespacecontents
A0000287molecular_functionmagnesium ion binding
A0008168molecular_functionmethyltransferase activity
A0008169molecular_functionC-methyltransferase activity
A0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
A0032259biological_processmethylation
A0042214biological_processterpene metabolic process
A1904047molecular_functionS-adenosyl-L-methionine binding
B0000287molecular_functionmagnesium ion binding
B0008168molecular_functionmethyltransferase activity
B0008169molecular_functionC-methyltransferase activity
B0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
B0032259biological_processmethylation
B0042214biological_processterpene metabolic process
B1904047molecular_functionS-adenosyl-L-methionine binding
C0000287molecular_functionmagnesium ion binding
C0008168molecular_functionmethyltransferase activity
C0008169molecular_functionC-methyltransferase activity
C0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
C0032259biological_processmethylation
C0042214biological_processterpene metabolic process
C1904047molecular_functionS-adenosyl-L-methionine binding
D0000287molecular_functionmagnesium ion binding
D0008168molecular_functionmethyltransferase activity
D0008169molecular_functionC-methyltransferase activity
D0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
D0032259biological_processmethylation
D0042214biological_processterpene metabolic process
D1904047molecular_functionS-adenosyl-L-methionine binding
E0000287molecular_functionmagnesium ion binding
E0008168molecular_functionmethyltransferase activity
E0008169molecular_functionC-methyltransferase activity
E0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
E0032259biological_processmethylation
E0042214biological_processterpene metabolic process
E1904047molecular_functionS-adenosyl-L-methionine binding
F0000287molecular_functionmagnesium ion binding
F0008168molecular_functionmethyltransferase activity
F0008169molecular_functionC-methyltransferase activity
F0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
F0032259biological_processmethylation
F0042214biological_processterpene metabolic process
F1904047molecular_functionS-adenosyl-L-methionine binding
G0000287molecular_functionmagnesium ion binding
G0008168molecular_functionmethyltransferase activity
G0008169molecular_functionC-methyltransferase activity
G0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
G0032259biological_processmethylation
G0042214biological_processterpene metabolic process
G1904047molecular_functionS-adenosyl-L-methionine binding
H0000287molecular_functionmagnesium ion binding
H0008168molecular_functionmethyltransferase activity
H0008169molecular_functionC-methyltransferase activity
H0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
H0032259biological_processmethylation
H0042214biological_processterpene metabolic process
H1904047molecular_functionS-adenosyl-L-methionine binding
I0000287molecular_functionmagnesium ion binding
I0008168molecular_functionmethyltransferase activity
I0008169molecular_functionC-methyltransferase activity
I0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
I0032259biological_processmethylation
I0042214biological_processterpene metabolic process
I1904047molecular_functionS-adenosyl-L-methionine binding
J0000287molecular_functionmagnesium ion binding
J0008168molecular_functionmethyltransferase activity
J0008169molecular_functionC-methyltransferase activity
J0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
J0032259biological_processmethylation
J0042214biological_processterpene metabolic process
J1904047molecular_functionS-adenosyl-L-methionine binding
K0000287molecular_functionmagnesium ion binding
K0008168molecular_functionmethyltransferase activity
K0008169molecular_functionC-methyltransferase activity
K0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
K0032259biological_processmethylation
K0042214biological_processterpene metabolic process
K1904047molecular_functionS-adenosyl-L-methionine binding
L0000287molecular_functionmagnesium ion binding
L0008168molecular_functionmethyltransferase activity
L0008169molecular_functionC-methyltransferase activity
L0008757molecular_functionS-adenosylmethionine-dependent methyltransferase activity
L0032259biological_processmethylation
L0042214biological_processterpene metabolic process
L1904047molecular_functionS-adenosyl-L-methionine binding
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 301
ChainResidue
AASN37
AGST303
AHOH401
AHOH402
AHOH403

site_idAC2
Number of Residues23
DetailsBINDING SITE FOR RESIDUE SAH A 302
ChainResidue
AHIS50
AGLY105
AGLY107
ATHR127
ALEU128
AGLN132
ACYS154
AASN155
AMET156
AASN172
AGLU173
ASER174
ATYR177
AVAL178
AHOH457
AHOH458
AHOH463
AHOH468
AHOH507
AGLN22
ATRP29
AHIS48
AHIS49

site_idAC3
Number of Residues17
DetailsBINDING SITE FOR RESIDUE GST A 303
ChainResidue
ATRP29
AARG34
AVAL36
AASN37
AHIS49
AHIS50
ATYR51
ATYR177
AGLY202
APHE222
AARG260
APHE282
AMG301
AHOH401
AHOH402
AHOH403
AHOH461

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL A 304
ChainResidue
ATHR19
AASN155
ALEU157
AHOH421
AHOH526

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 305
ChainResidue
AASP179
ALEU180
AHIS181
AHIS227
AGLU231
AHOH519

site_idAC6
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 306
ChainResidue
APRO206
AGLY209
AGLN210
AARG230
AHOH498
DVAL292
EASP179
EGOL306
EHOH420

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG B 301
ChainResidue
BASN37
BGST303
BHOH401
BHOH402
BHOH403

site_idAC8
Number of Residues21
DetailsBINDING SITE FOR RESIDUE SAH B 302
ChainResidue
BGLN22
BTRP29
BHIS49
BHIS50
BGLY105
BGLY107
BTHR127
BLEU128
BGLN132
BCYS154
BASN155
BMET156
BASN172
BGLU173
BSER174
BTYR177
BHOH449
BHOH451
BHOH452
BHOH455
BHOH456

site_idAC9
Number of Residues15
DetailsBINDING SITE FOR RESIDUE GST B 303
ChainResidue
BPHE222
BARG260
BPHE282
BMG301
BHOH401
BHOH403
BHOH437
BTRP29
BARG34
BVAL36
BASN37
BHIS49
BHIS50
BTYR51
BTYR177

site_idBC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL B 304
ChainResidue
BPRO206
BGLY209
BGLN210
BARG230
BHOH433
BHOH503
FASP179

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG C 301
ChainResidue
CASN37
CGST303
CHOH401
CHOH402
CHOH403

site_idBC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE SAH C 302
ChainResidue
CGLN22
CTRP29
CHIS49
CHIS50
CGLY105
CGLY107
CTHR127
CLEU128
CGLN132
CCYS154
CASN155
CMET156
CASN172
CGLU173
CSER174
CTYR177
CVAL178
CHOH441
CHOH443
CHOH447
CHOH448
CHOH468

site_idBC4
Number of Residues14
DetailsBINDING SITE FOR RESIDUE GST C 303
ChainResidue
CTRP29
CARG34
CVAL36
CASN37
CHIS49
CHIS50
CTYR51
CTYR177
CPHE222
CARG260
CMG301
CHOH401
CHOH403
CHOH484

site_idBC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL C 304
ChainResidue
CGLU86
CMET114
CARG117
CARG118

site_idBC6
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL C 305
ChainResidue
CTYR28
CASN31
CGLU32
CARG34
CHOH455
CHOH486
CHOH531
KILE145
KHOH505

site_idBC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG D 301
ChainResidue
DASN37
DGST303
DHOH401
DHOH402
DHOH403

site_idBC8
Number of Residues20
DetailsBINDING SITE FOR RESIDUE SAH D 302
ChainResidue
DGLN22
DTRP29
DHIS49
DHIS50
DGLY105
DGLY107
DTHR127
DLEU128
DGLN132
DCYS154
DASN155
DMET156
DASN172
DSER174
DTYR177
DHOH451
DHOH452
DHOH453
DHOH462
DHOH478

site_idBC9
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GST D 303
ChainResidue
DTRP29
DARG34
DVAL36
DASN37
DHIS49
DHIS50
DTYR51
DTYR177
DPHE222
DARG260
DPHE282
DMG301
DHOH401
DHOH402
DHOH403
DHOH470

site_idCC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL D 304
ChainResidue
CASP179
CHOH521
DPRO206
DGLY209
DGLN210
DARG230
DHOH419
DHOH524

site_idCC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG E 301
ChainResidue
EASN37
EGST303
EHOH401
EHOH402
EHOH403

site_idCC3
Number of Residues21
DetailsBINDING SITE FOR RESIDUE SAH E 302
ChainResidue
EGLN22
ETRP29
EHIS49
EHIS50
EGLY105
EGLY107
ETHR127
ELEU128
EGLN132
ECYS154
EASN155
EMET156
EASN172
ESER174
ETYR177
EVAL178
EHOH443
EHOH444
EHOH445
EHOH447
EHOH490

site_idCC4
Number of Residues17
DetailsBINDING SITE FOR RESIDUE GST E 303
ChainResidue
ETRP29
EVAL36
EASN37
EHIS49
EHIS50
ETYR51
ETYR177
EGLY202
EPHE222
EARG260
EPHE282
EMG301
EHOH401
EHOH403
EHOH450
EHOH511
EHOH513

site_idCC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SO4 E 304
ChainResidue
ETYR28
EARG34
EHIS221
EHOH450
EHOH492
EHOH511
HARG138
HHOH453
HHOH474

site_idCC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL E 305
ChainResidue
EPHE135
EARG138
EARG139
EGLU142
EHOH515
EHOH530
HARG39
HILE74

site_idCC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL E 306
ChainResidue
AGLY209
AGOL306
ETHR19
EASN155
ELEU157
EASP182
EHOH420
EHOH433

site_idCC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG F 301
ChainResidue
FASN37
FGST303
FHOH401
FHOH402
FHOH403

site_idCC9
Number of Residues23
DetailsBINDING SITE FOR RESIDUE SAH F 302
ChainResidue
FGLN22
FTRP29
FHIS49
FHIS50
FGLY105
FCYS106
FGLY107
FTHR127
FLEU128
FGLN132
FCYS154
FASN155
FMET156
FASN172
FGLU173
FSER174
FTYR177
FVAL178
FHOH425
FHOH431
FHOH434
FHOH440
FHOH447

site_idDC1
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GST F 303
ChainResidue
FTRP29
FARG34
FASN37
FHIS49
FHIS50
FTYR51
FMET176
FTYR177
FGLY202
FPHE222
FARG260
FPHE282
FMG301
FHOH401
FHOH403
FHOH484

site_idDC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL F 304
ChainResidue
BHOH443
CVAL292
FTRP204
FPRO206
FGLY209
FGLN210
FARG230
FHOH460

site_idDC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG G 301
ChainResidue
GASN37
GGST303
GHOH401
GHOH402
GHOH403

site_idDC4
Number of Residues22
DetailsBINDING SITE FOR RESIDUE SAH G 302
ChainResidue
GGLN22
GTRP29
GHIS48
GHIS49
GHIS50
GGLY105
GGLY107
GTHR127
GLEU128
GGLN132
GCYS154
GASN155
GMET156
GASN172
GGLU173
GSER174
GTYR177
GHOH451
GHOH452
GHOH453
GHOH455
GHOH460

site_idDC5
Number of Residues17
DetailsBINDING SITE FOR RESIDUE GST G 303
ChainResidue
GTRP29
GARG34
GVAL36
GASN37
GHIS49
GHIS50
GTYR51
GGLU173
GTYR177
GPHE222
GARG260
GPHE282
GMG301
GHOH401
GHOH403
GHOH463
GHOH507

site_idDC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE GOL G 304
ChainResidue
GGLY209
GGLN210
GARG230
GHOH461
GHOH522
JARG240
JVAL292
LASP179
LASP182
LHOH497

site_idDC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG H 301
ChainResidue
HASN37
HGST303
HHOH401
HHOH402
HHOH403

site_idDC8
Number of Residues23
DetailsBINDING SITE FOR RESIDUE SAH H 302
ChainResidue
HGLN22
HTRP29
HHIS48
HHIS49
HHIS50
HGLY105
HGLY107
HTHR127
HLEU128
HGLN132
HCYS154
HASN155
HMET156
HASN172
HGLU173
HSER174
HTYR177
HVAL178
HHOH465
HHOH466
HHOH468
HHOH476
HHOH481

site_idDC9
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GST H 303
ChainResidue
HTRP29
HARG34
HVAL36
HASN37
HHIS49
HHIS50
HTYR51
HTYR177
HPHE222
HARG260
HPHE282
HMG301
HHOH401
HHOH402
HHOH403
HHOH471

site_idEC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL H 304
ChainResidue
HTRP204
HPRO206
HGLY209
HGLN210
HARG230
HHOH408
JHOH431

site_idEC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG I 301
ChainResidue
IASN37
IGST303
IGOL304
IHOH401
IHOH402

site_idEC3
Number of Residues23
DetailsBINDING SITE FOR RESIDUE SAH I 302
ChainResidue
IGLN22
ITRP29
IHIS48
IHIS49
IHIS50
IGLY105
IGLY107
ITHR127
ILEU128
IGLN132
ICYS154
IASN155
IMET156
IASN172
IGLU173
ISER174
ITYR177
IVAL178
IHOH442
IHOH445
IHOH447
IHOH449
IHOH490

site_idEC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GST I 303
ChainResidue
ITRP29
IARG34
IASN37
IHIS49
ITYR51
IGLU173
ITYR177
IPHE222
IARG260
IMG301
IGOL304
IHOH401
IHOH402
IHOH427
IHOH461
IHOH497

site_idEC5
Number of Residues12
DetailsBINDING SITE FOR RESIDUE GOL I 304
ChainResidue
IARG34
IVAL36
IASN37
ILEU77
IGLU81
ITYR256
IARG260
ILEU265
IMG301
IGST303
IHOH401
IHOH402

site_idEC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG J 301
ChainResidue
JASN37
JGST303
JHOH401
JHOH402
JHOH403

site_idEC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE SAH J 302
ChainResidue
JGLN22
JTRP29
JHIS49
JHIS50
JGLY105
JGLY107
JTHR127
JLEU128
JGLN132
JCYS154
JASN155
JMET156
JASN172
JGLU173
JSER174
JTYR177
JVAL178
JHOH449
JHOH450
JHOH451
JHOH452
JHOH453

site_idEC8
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GST J 303
ChainResidue
JTRP29
JARG34
JVAL36
JASN37
JHIS49
JHIS50
JTYR51
JTYR177
JPHE222
JARG260
JPHE282
JMG301
JHOH401
JHOH402
JHOH403
JHOH479

site_idEC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL J 304
ChainResidue
JASP179
JLEU180
JHIS181
JHIS227
JGLU231
JHOH531

site_idFC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG K 301
ChainResidue
KASN37
KGST303
KHOH401
KHOH402
KHOH403

site_idFC2
Number of Residues22
DetailsBINDING SITE FOR RESIDUE SAH K 302
ChainResidue
KGLN22
KTRP29
KHIS48
KHIS49
KHIS50
KGLY105
KGLY107
KTHR127
KLEU128
KGLN132
KCYS154
KASN155
KMET156
KASN172
KSER174
KTYR177
KVAL178
KHOH439
KHOH444
KHOH468
KHOH476
KHOH486

site_idFC3
Number of Residues17
DetailsBINDING SITE FOR RESIDUE GST K 303
ChainResidue
KTRP29
KARG34
KVAL36
KASN37
KHIS49
KHIS50
KTYR51
KTYR177
KGLY202
KPHE222
KARG260
KPHE282
KMG301
KHOH401
KHOH402
KHOH403
KHOH442

site_idFC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG L 301
ChainResidue
LASN37
LGST303
LHOH401
LHOH402
LHOH403

site_idFC5
Number of Residues22
DetailsBINDING SITE FOR RESIDUE SAH L 302
ChainResidue
LGLN22
LTRP29
LHIS49
LHIS50
LGLY105
LGLY107
LTHR127
LLEU128
LGLN132
LCYS154
LASN155
LMET156
LASN172
LGLU173
LSER174
LTYR177
LVAL178
LHOH442
LHOH443
LHOH445
LHOH450
LHOH451

site_idFC6
Number of Residues16
DetailsBINDING SITE FOR RESIDUE GST L 303
ChainResidue
LTRP29
LARG34
LVAL36
LASN37
LHIS49
LHIS50
LTYR51
LTYR177
LGLY202
LPHE222
LARG260
LPHE282
LMG301
LHOH401
LHOH403
LHOH456

site_idFC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL L 304
ChainResidue
LASP179
LLEU180
LHIS181
LHIS227
LGLU231
LHOH501
LHOH513

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PDB entries from 2024-07-24

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