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4QII

Crystal Structure of type II MenB from Mycobacteria tuberculosis

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 Residues26
DetailsBINDING SITE FOR RESIDUE 2NE A 401
ChainResidue
AVAL57
AILE136
ATRP157
AGLY160
AGLY161
ATHR184
AASP185
AVAL188
ASER190
AHOH597
AHOH600
AARG58
AHOH709
AHOH737
FPHE299
FLYS302
FHOH577
GALA14
GLEU15
AALA60
APHE61
ASER103
AGLY104
AGLY105
AASP106
AGLN107

site_idAC2
Number of Residues35
DetailsBINDING SITE FOR RESIDUE 2NE B 401
ChainResidue
BGLU56
BVAL57
BARG58
BALA60
BLYS95
BSER103
BGLY104
BGLY105
BASP106
BGLN107
BTYR115
BTRP157
BGLY161
BTHR184
BASP185
BVAL188
BSER190
BHOH542
BHOH601
BHOH608
BHOH627
BHOH637
BHOH638
BHOH648
BHOH692
BHOH699
BHOH707
BHOH737
BHOH789
BHOH817
EPHE299
ELYS302
EHOH533
IALA14
ILEU15

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PGE B 402
ChainResidue
AVAL204
BARG202
BMET227
BHOH683
CGLN203

site_idAC4
Number of Residues29
DetailsBINDING SITE FOR RESIDUE 2NE C 401
ChainResidue
CVAL57
CARG58
CALA60
CSER103
CGLY104
CGLY105
CASP106
CGLN107
CTRP157
CGLY160
CGLY161
CTHR184
CASP185
CSER190
CHOH547
CHOH625
CHOH632
CHOH643
CHOH648
CHOH652
CHOH679
CHOH683
CHOH749
CHOH819
DPHE299
DLYS302
DHOH651
HALA14
HLEU15

site_idAC5
Number of Residues24
DetailsBINDING SITE FOR RESIDUE 2NE D 401
ChainResidue
DGLU56
DVAL57
DARG58
DALA60
DSER103
DGLY104
DGLY105
DASP106
DGLN107
DTYR115
DTRP157
DGLY161
DTHR184
DASP185
DSER190
DHOH614
DHOH619
DHOH647
DHOH667
DHOH697
ASER119
CTYR287
CPHE299
CLYS302

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PGE D 402
ChainResidue
DARG202
DGLN203
DMET227
DHOH515
DHOH718
EMET227

site_idAC7
Number of Residues34
DetailsBINDING SITE FOR RESIDUE 2NE E 401
ChainResidue
BTYR287
BPHE299
BLYS302
BHOH571
EGLU56
EVAL57
EARG58
EALA60
ELYS95
ESER103
EGLY104
EGLY105
EASP106
EGLN107
ETYR115
ETRP157
EGLY161
ETHR184
EASP185
EVAL188
ESER190
EHOH530
EHOH542
EHOH621
EHOH635
EHOH703
EHOH708
EHOH709
EHOH717
EHOH740
EHOH795
EHOH808
EHOH813
EHOH819

site_idAC8
Number of Residues31
DetailsBINDING SITE FOR RESIDUE 2NE F 401
ChainResidue
ATYR287
APHE299
ALYS302
AHOH678
FGLU56
FVAL57
FARG58
FALA60
FLYS95
FSER103
FGLY104
FGLY105
FASP106
FGLN107
FTYR115
FTRP157
FGLY161
FTHR184
FASP185
FVAL188
FSER190
FHOH561
FHOH563
FHOH584
FHOH617
FHOH680
FHOH723
FHOH727
FHOH751
FHOH784
FHOH796

site_idAC9
Number of Residues31
DetailsBINDING SITE FOR RESIDUE 2NE G 401
ChainResidue
ALEU15
GVAL57
GARG58
GALA60
GLYS95
GSER103
GGLY104
GGLY105
GASP106
GGLN107
GTYR115
GTRP157
GGLY161
GTHR184
GASP185
GSER190
GHOH536
GHOH588
GHOH599
GHOH610
GHOH635
GHOH636
GHOH656
GHOH680
GHOH707
GHOH721
GHOH726
LPHE299
LLYS302
LHOH588
LHOH774

site_idBC1
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PGE G 402
ChainResidue
GALA201
GARG202
GGLN203
GMET227
GHOH629
HHOH758
IARG202
IVAL204
IMET227

site_idBC2
Number of Residues34
DetailsBINDING SITE FOR RESIDUE 2NE H 401
ChainResidue
CALA14
CLEU15
HVAL57
HARG58
HALA60
HLYS95
HSER103
HGLY104
HGLY105
HASP106
HGLN107
HTYR115
HLEU134
HTRP157
HGLY161
HTHR184
HASP185
HSER190
HHOH512
HHOH540
HHOH588
HHOH633
HHOH647
HHOH665
HHOH669
HHOH692
HHOH714
HHOH751
HHOH774
KTYR287
KPHE299
KLYS302
KHOH582
KHOH721

site_idBC3
Number of Residues35
DetailsBINDING SITE FOR RESIDUE 2NE I 401
ChainResidue
BALA14
BLEU15
IVAL57
IARG58
IALA60
ILYS95
ISER103
IGLY104
IGLY105
IASP106
IGLN107
ITYR115
ILEU134
ITRP157
IGLY161
ITHR184
IASP185
IVAL188
ISER190
IHOH544
IHOH573
IHOH579
IHOH651
IHOH660
IHOH673
IHOH678
IHOH725
IHOH732
IHOH777
IHOH826
JTYR287
JPHE299
JLYS302
JHOH575
JHOH602

site_idBC4
Number of Residues26
DetailsBINDING SITE FOR RESIDUE 2NE J 401
ChainResidue
IPHE299
ILYS302
IHOH656
JVAL57
JARG58
JSER103
JGLY104
JGLY105
JASP106
JGLN107
JTYR115
JTRP157
JGLY161
JTHR184
JASP185
JVAL188
JSER190
JHOH564
JHOH627
JHOH688
JHOH692
JHOH712
JHOH720
JHOH724
JHOH743
JHOH753

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PGE J 402
ChainResidue
JARG202
JHOH542
JHOH623
JHOH674
KARG202
LARG202

site_idBC6
Number of Residues28
DetailsBINDING SITE FOR RESIDUE 2NE K 401
ChainResidue
HTYR287
HPHE299
HLYS302
HHOH656
KGLU56
KVAL57
KARG58
KALA60
KLYS95
KSER103
KGLY104
KGLY105
KASP106
KGLN107
KTYR115
KTRP157
KGLY161
KTHR184
KASP185
KVAL188
KSER190
KHOH572
KHOH608
KHOH621
KHOH674
KHOH675
KHOH725
KHOH741

site_idBC7
Number of Residues26
DetailsBINDING SITE FOR RESIDUE 2NE L 401
ChainResidue
GTYR287
GPHE299
GLYS302
GHOH683
LGLU56
LVAL57
LARG58
LALA60
LLYS95
LSER103
LGLY104
LGLY105
LASP106
LGLN107
LTYR115
LTRP157
LGLY161
LTHR184
LASP185
LSER190
LHOH572
LHOH623
LHOH636
LHOH706
LHOH778
LHOH783

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
KARG58
LARG58
AARG58
BARG58
CARG58
DARG58
EARG58
FARG58
GARG58
HARG58
IARG58
JARG58

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

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
DSER103
ESER103
FSER103
GSER103
HSER103
ISER103
JSER103
KSER103
LSER103
ASER103
BSER103
CSER103

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

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

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

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

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

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
BASP185
CASP185
DASP185
EASP185
FASP185
GASP185
HASP185
IASP185
JASP185
KASP185
LASP185

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
BTYR287
CTYR287
DTYR287
ETYR287
FTYR287
GTYR287
HTYR287
ITYR287
JTYR287
KTYR287
LTYR287

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_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
FGLY161electrostatic stabiliser, hydrogen bond donor
FASP185activator
FSER190activator
FTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role
FGLY105electrostatic stabiliser, hydrogen bond donor
FTYR115electrostatic stabiliser, hydrogen bond 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

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
KGLY161electrostatic stabiliser, hydrogen bond donor
KSER190activator
KTYR287electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role
KGLY105electrostatic stabiliser, hydrogen bond donor
KTYR115electrostatic stabiliser, hydrogen bond donor, steric role
KASP185activator

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

219869

PDB entries from 2024-05-15

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