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4QIJ

Crystal structure of MenB from Mycobacteria tuberculosis in complex with 1-HNA-CoA

Functional Information from GO Data
ChainGOidnamespacecontents
A0005886cellular_componentplasma membrane
A0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
A0009234biological_processmenaquinone biosynthetic process
A0016829molecular_functionlyase activity
A0034214biological_processprotein hexamerization
B0005886cellular_componentplasma membrane
B0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
B0009234biological_processmenaquinone biosynthetic process
B0016829molecular_functionlyase activity
B0034214biological_processprotein hexamerization
C0005886cellular_componentplasma membrane
C0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
C0009234biological_processmenaquinone biosynthetic process
C0016829molecular_functionlyase activity
C0034214biological_processprotein hexamerization
D0005886cellular_componentplasma membrane
D0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
D0009234biological_processmenaquinone biosynthetic process
D0016829molecular_functionlyase activity
D0034214biological_processprotein hexamerization
E0005886cellular_componentplasma membrane
E0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
E0009234biological_processmenaquinone biosynthetic process
E0016829molecular_functionlyase activity
E0034214biological_processprotein hexamerization
F0005886cellular_componentplasma membrane
F0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
F0009234biological_processmenaquinone biosynthetic process
F0016829molecular_functionlyase activity
F0034214biological_processprotein hexamerization
G0005886cellular_componentplasma membrane
G0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
G0009234biological_processmenaquinone biosynthetic process
G0016829molecular_functionlyase activity
G0034214biological_processprotein hexamerization
H0005886cellular_componentplasma membrane
H0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
H0009234biological_processmenaquinone biosynthetic process
H0016829molecular_functionlyase activity
H0034214biological_processprotein hexamerization
I0005886cellular_componentplasma membrane
I0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
I0009234biological_processmenaquinone biosynthetic process
I0016829molecular_functionlyase activity
I0034214biological_processprotein hexamerization
J0005886cellular_componentplasma membrane
J0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
J0009234biological_processmenaquinone biosynthetic process
J0016829molecular_functionlyase activity
J0034214biological_processprotein hexamerization
K0005886cellular_componentplasma membrane
K0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
K0009234biological_processmenaquinone biosynthetic process
K0016829molecular_functionlyase activity
K0034214biological_processprotein hexamerization
L0005886cellular_componentplasma membrane
L0008935molecular_function1,4-dihydroxy-2-naphthoyl-CoA synthase activity
L0009234biological_processmenaquinone biosynthetic process
L0016829molecular_functionlyase activity
L0034214biological_processprotein hexamerization
Functional Information from PDB Data
site_idAC1
Number of Residues29
DetailsBINDING SITE FOR RESIDUE 1HA A 401
ChainResidue
AGLU56
AASP106
AGLN107
ATYR115
ALEU134
AILE136
ATRP157
AGLY161
ATHR184
AASP185
ASER190
AVAL57
AHOH602
AHOH605
AHOH617
AHOH685
FPHE299
FLYS302
FHOH649
LALA14
LLEU15
LHOH576
AARG58
AALA60
APHE61
ALYS95
ASER103
AGLY104
AGLY105

site_idAC2
Number of Residues33
DetailsBINDING SITE FOR RESIDUE 1HA B 401
ChainResidue
BGLU56
BVAL57
BARG58
BALA60
BLYS95
BSER103
BGLY104
BGLY105
BASP106
BGLN107
BTYR115
BILE136
BLEU137
BTRP157
BGLY161
BTHR184
BASP185
BSER190
BPHE191
BHOH518
BHOH551
BHOH567
BHOH578
BHOH591
BHOH608
BHOH655
BHOH688
BHOH694
BHOH707
EPHE299
ELYS302
KALA14
KLEU15

site_idAC3
Number of Residues32
DetailsBINDING SITE FOR RESIDUE 1HA C 401
ChainResidue
CGLU56
CVAL57
CARG58
CALA60
CLYS95
CSER103
CGLY104
CGLY105
CASP106
CGLN107
CTYR115
CILE136
CLEU137
CTRP157
CGLY161
CTHR184
CASP185
CSER190
CPHE191
CHOH525
CHOH532
CHOH579
CHOH584
CHOH585
CHOH623
CHOH625
CHOH638
CHOH685
DPHE299
DLYS302
JALA14
JLEU15

site_idAC4
Number of Residues27
DetailsBINDING SITE FOR RESIDUE 1HA D 401
ChainResidue
DALA60
DLYS95
DSER103
DGLY104
DGLY105
DASP106
DGLN107
DTYR115
DILE136
DTRP157
DGLY161
DTHR184
DASP185
DSER190
DPHE191
DHOH604
DHOH618
DHOH628
DHOH649
IHOH585
IHOH616
IHOH701
CPHE299
CLYS302
CHOH630
DVAL57
DARG58

site_idAC5
Number of Residues27
DetailsBINDING SITE FOR RESIDUE 1HA E 401
ChainResidue
BPHE299
BLYS302
EGLU56
EVAL57
EARG58
EALA60
ELYS95
ESER103
EGLY104
EGLY105
EASP106
EGLN107
EILE136
ELEU137
ETRP157
EGLY160
EGLY161
ETHR184
EASP185
EVAL188
ESER190
EPHE191
EASP192
EHOH562
EHOH568
EHOH576
EHOH611

site_idAC6
Number of Residues28
DetailsBINDING SITE FOR RESIDUE 1HA F 401
ChainResidue
APHE299
ALYS302
FGLU56
FVAL57
FARG58
FALA60
FLYS95
FSER103
FGLY104
FGLY105
FASP106
FGLN107
FTYR115
FILE136
FLEU137
FTRP157
FGLY161
FTHR184
FASP185
FVAL188
FSER190
FPHE191
FHOH512
FHOH517
FHOH539
FHOH550
FHOH553
FHOH612

site_idAC7
Number of Residues24
DetailsBINDING SITE FOR RESIDUE 1HA G 401
ChainResidue
GGLU56
GVAL57
GARG58
GALA60
GLYS95
GSER103
GGLY104
GGLY105
GASP106
GGLN107
GTYR115
GLEU137
GTRP157
GGLY161
GTHR184
GASP185
GVAL188
GSER190
GPHE191
GHOH537
GHOH594
KPHE299
KLYS302
LSER119

site_idAC8
Number of Residues27
DetailsBINDING SITE FOR RESIDUE 1HA H 401
ChainResidue
HGLU56
HVAL57
HARG58
HALA60
HLYS95
HSER103
HGLY104
HGLY105
HASP106
HGLN107
HTYR115
HILE136
HLEU137
HTRP157
HGLY161
HTHR184
HASP185
HVAL188
HSER190
HPHE191
HHOH547
HHOH623
HHOH631
HHOH642
JPHE299
JLYS302
JHOH580

site_idAC9
Number of Residues34
DetailsBINDING SITE FOR RESIDUE 1HA I 401
ChainResidue
IGLU56
IVAL57
IARG58
IALA60
ILYS95
ISER103
IGLY104
IGLY105
IASP106
IGLN107
ITYR115
IILE136
ILEU137
ITRP157
IGLY160
IGLY161
ITHR184
IASP185
IVAL188
ISER190
IPHE191
IHOH526
IHOH558
IHOH569
IHOH584
IHOH599
IHOH601
IHOH614
IHOH655
IHOH666
IHOH679
IHOH681
LPHE299
LLYS302

site_idBC1
Number of Residues31
DetailsBINDING SITE FOR RESIDUE 1HA J 401
ChainResidue
CALA14
CLEU15
HPHE299
HLYS302
JGLU56
JVAL57
JARG58
JALA60
JLYS95
JSER103
JGLY104
JGLY105
JASP106
JGLN107
JTYR115
JILE136
JTRP157
JGLY161
JTHR184
JASP185
JVAL188
JSER190
JPHE191
JHOH514
JHOH545
JHOH554
JHOH557
JHOH594
JHOH612
JHOH672
JHOH722

site_idBC2
Number of Residues33
DetailsBINDING SITE FOR RESIDUE 1HA K 401
ChainResidue
BALA14
BLEU15
GPHE299
GLYS302
GHOH584
KGLU56
KVAL57
KARG58
KALA60
KLYS95
KSER103
KGLY104
KGLY105
KASP106
KGLN107
KTYR115
KILE136
KLEU137
KTRP157
KGLY160
KGLY161
KTHR184
KASP185
KSER190
KPHE191
KHOH521
KHOH524
KHOH559
KHOH580
KHOH589
KHOH665
KHOH673
KHOH695

site_idBC3
Number of Residues31
DetailsBINDING SITE FOR RESIDUE 1HA L 401
ChainResidue
AALA14
ALEU15
IPHE299
ILYS302
IHOH595
LVAL57
LARG58
LALA60
LSER103
LGLY104
LGLY105
LASP106
LGLN107
LTYR115
LTRP157
LGLY161
LTHR184
LASP185
LVAL188
LSER190
LPHE191
LHOH565
LHOH617
LHOH624
LHOH632
LHOH663
LHOH723
LHOH724
LHOH728
LHOH732
LHOH748

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:21830810
ChainResidueDetails
AARG58
JARG58
KARG58
LARG58
BARG58
CARG58
DARG58
EARG58
FARG58
GARG58
HARG58
IARG58

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING: in other chain => ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:21830810
ChainResidueDetails
ALYS95
JLYS95
KLYS95
LLYS95
BLYS95
CLYS95
DLYS95
ELYS95
FLYS95
GLYS95
HLYS95
ILYS95

site_idSWS_FT_FI3
Number of Residues12
DetailsBINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628, ECO:0000269|PubMed:16131752, ECO:0000269|PubMed:21830810
ChainResidueDetails
ASER103
JSER103
KSER103
LSER103
BSER103
CSER103
DSER103
ESER103
FSER103
GSER103
HSER103
ISER103

site_idSWS_FT_FI4
Number of Residues12
DetailsBINDING: in other chain => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934
ChainResidueDetails
ATYR115
JTYR115
KTYR115
LTYR115
BTYR115
CTYR115
DTYR115
ETYR115
FTYR115
GTYR115
HTYR115
ITYR115

site_idSWS_FT_FI5
Number of Residues24
DetailsBINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000269|PubMed:12909628
ChainResidueDetails
ATRP157
ETHR184
FTRP157
FTHR184
GTRP157
GTHR184
HTRP157
HTHR184
ITRP157
ITHR184
JTRP157
ATHR184
JTHR184
KTRP157
KTHR184
LTRP157
LTHR184
BTRP157
BTHR184
CTRP157
CTHR184
DTRP157
DTHR184
ETRP157

site_idSWS_FT_FI6
Number of Residues12
DetailsBINDING: in other chain => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:21830810
ChainResidueDetails
ASER190
JSER190
KSER190
LSER190
BSER190
CSER190
DSER190
ESER190
FSER190
GSER190
HSER190
ISER190

site_idSWS_FT_FI7
Number of Residues24
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934
ChainResidueDetails
ATYR287
ELYS302
FTYR287
FLYS302
GTYR287
GLYS302
HTYR287
HLYS302
ITYR287
ILYS302
JTYR287
ALYS302
JLYS302
KTYR287
KLYS302
LTYR287
LLYS302
BTYR287
BLYS302
CTYR287
CLYS302
DTYR287
DLYS302
ETYR287

site_idSWS_FT_FI8
Number of Residues12
DetailsSITE: Important for catalysis => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934
ChainResidueDetails
ATYR115
JTYR115
KTYR115
LTYR115
BTYR115
CTYR115
DTYR115
ETYR115
FTYR115
GTYR115
HTYR115
ITYR115

site_idSWS_FT_FI9
Number of Residues12
DetailsSITE: Important for catalysis => ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:20643650, ECO:0000305|PubMed:21830810
ChainResidueDetails
AASP185
JASP185
KASP185
LASP185
BASP185
CASP185
DASP185
EASP185
FASP185
GASP185
HASP185
IASP185

site_idSWS_FT_FI10
Number of Residues12
DetailsSITE: Important for catalysis => ECO:0000250|UniProtKB:P0ABU0, ECO:0000255|HAMAP-Rule:MF_01934, ECO:0000305|PubMed:12909628
ChainResidueDetails
ATYR287
JTYR287
KTYR287
LTYR287
BTYR287
CTYR287
DTYR287
ETYR287
FTYR287
GTYR287
HTYR287
ITYR287

Catalytic Information from CSA
site_idMCSA1
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
AGLY105electrostatic stabiliser, hydrogen bond donor
ATYR115electrostatic stabiliser, hydrogen bond donor, steric role
AGLY161electrostatic stabiliser, hydrogen bond donor
AASP185activator
ASER190activator
ATYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA10
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
JGLY105electrostatic stabiliser, hydrogen bond donor
JTYR115electrostatic stabiliser, hydrogen bond donor, steric role
JGLY161electrostatic stabiliser, hydrogen bond donor
JASP185activator
JSER190activator
JTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA11
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
KGLY105electrostatic stabiliser, hydrogen bond donor
KTYR115electrostatic stabiliser, hydrogen bond donor, steric role
KGLY161electrostatic stabiliser, hydrogen bond donor
KASP185activator
KSER190activator
KTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA12
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
LGLY105electrostatic stabiliser, hydrogen bond donor
LTYR115electrostatic stabiliser, hydrogen bond donor, steric role
LGLY161electrostatic stabiliser, hydrogen bond donor
LASP185activator
LSER190activator
LTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA2
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
BGLY105electrostatic stabiliser, hydrogen bond donor
BTYR115electrostatic stabiliser, hydrogen bond donor, steric role
BGLY161electrostatic stabiliser, hydrogen bond donor
BASP185activator
BSER190activator
BTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA3
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
CGLY105electrostatic stabiliser, hydrogen bond donor
CTYR115electrostatic stabiliser, hydrogen bond donor, steric role
CGLY161electrostatic stabiliser, hydrogen bond donor
CASP185activator
CSER190activator
CTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA4
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
DGLY105electrostatic stabiliser, hydrogen bond donor
DTYR115electrostatic stabiliser, hydrogen bond donor, steric role
DGLY161electrostatic stabiliser, hydrogen bond donor
DASP185activator
DSER190activator
DTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA5
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
EGLY105electrostatic stabiliser, hydrogen bond donor
ETYR115electrostatic stabiliser, hydrogen bond donor, steric role
EGLY161electrostatic stabiliser, hydrogen bond donor
EASP185activator
ESER190activator
ETYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA6
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
FGLY105electrostatic stabiliser, hydrogen bond donor
FTYR115electrostatic stabiliser, hydrogen bond donor, steric role
FGLY161electrostatic stabiliser, hydrogen bond donor
FASP185activator
FSER190activator
FTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA7
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
GGLY105electrostatic stabiliser, hydrogen bond donor
GTYR115electrostatic stabiliser, hydrogen bond donor, steric role
GGLY161electrostatic stabiliser, hydrogen bond donor
GASP185activator
GSER190activator
GTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA8
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
HGLY105electrostatic stabiliser, hydrogen bond donor
HTYR115electrostatic stabiliser, hydrogen bond donor, steric role
HGLY161electrostatic stabiliser, hydrogen bond donor
HASP185activator
HSER190activator
HTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_idMCSA9
Number of Residues6
DetailsM-CSA 346
ChainResidueDetails
IGLY105electrostatic stabiliser, hydrogen bond donor
ITYR115electrostatic stabiliser, hydrogen bond donor, steric role
IGLY161electrostatic stabiliser, hydrogen bond donor
IASP185activator
ISER190activator
ITYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

225946

PDB entries from 2024-10-09

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