Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4QII

Crystal Structure of type II MenB from Mycobacteria tuberculosis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005886	cellular_component	plasma membrane
A	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
A	0009234	biological_process	menaquinone biosynthetic process
A	0016829	molecular_function	lyase activity
A	0034214	biological_process	protein hexamerization
B	0005886	cellular_component	plasma membrane
B	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
B	0009234	biological_process	menaquinone biosynthetic process
B	0016829	molecular_function	lyase activity
B	0034214	biological_process	protein hexamerization
C	0005886	cellular_component	plasma membrane
C	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
C	0009234	biological_process	menaquinone biosynthetic process
C	0016829	molecular_function	lyase activity
C	0034214	biological_process	protein hexamerization
D	0005886	cellular_component	plasma membrane
D	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
D	0009234	biological_process	menaquinone biosynthetic process
D	0016829	molecular_function	lyase activity
D	0034214	biological_process	protein hexamerization
E	0005886	cellular_component	plasma membrane
E	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
E	0009234	biological_process	menaquinone biosynthetic process
E	0016829	molecular_function	lyase activity
E	0034214	biological_process	protein hexamerization
F	0005886	cellular_component	plasma membrane
F	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
F	0009234	biological_process	menaquinone biosynthetic process
F	0016829	molecular_function	lyase activity
F	0034214	biological_process	protein hexamerization
G	0005886	cellular_component	plasma membrane
G	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
G	0009234	biological_process	menaquinone biosynthetic process
G	0016829	molecular_function	lyase activity
G	0034214	biological_process	protein hexamerization
H	0005886	cellular_component	plasma membrane
H	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
H	0009234	biological_process	menaquinone biosynthetic process
H	0016829	molecular_function	lyase activity
H	0034214	biological_process	protein hexamerization
I	0005886	cellular_component	plasma membrane
I	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
I	0009234	biological_process	menaquinone biosynthetic process
I	0016829	molecular_function	lyase activity
I	0034214	biological_process	protein hexamerization
J	0005886	cellular_component	plasma membrane
J	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
J	0009234	biological_process	menaquinone biosynthetic process
J	0016829	molecular_function	lyase activity
J	0034214	biological_process	protein hexamerization
K	0005886	cellular_component	plasma membrane
K	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
K	0009234	biological_process	menaquinone biosynthetic process
K	0016829	molecular_function	lyase activity
K	0034214	biological_process	protein hexamerization
L	0005886	cellular_component	plasma membrane
L	0008935	molecular_function	1,4-dihydroxy-2-naphthoyl-CoA synthase activity
L	0009234	biological_process	menaquinone biosynthetic process
L	0016829	molecular_function	lyase activity
L	0034214	biological_process	protein hexamerization

Functional Information from PDB Data

site_id	AC1
Number of Residues	26
Details	BINDING SITE FOR RESIDUE 2NE A 401

Chain	Residue
A	VAL57
A	ILE136
A	TRP157
A	GLY160
A	GLY161
A	THR184
A	ASP185
A	VAL188
A	SER190
A	HOH597
A	HOH600
A	ARG58
A	HOH709
A	HOH737
F	PHE299
F	LYS302
F	HOH577
G	ALA14
G	LEU15
A	ALA60
A	PHE61
A	SER103
A	GLY104
A	GLY105
A	ASP106
A	GLN107

site_id	AC2
Number of Residues	35
Details	BINDING SITE FOR RESIDUE 2NE B 401

Chain	Residue
B	GLU56
B	VAL57
B	ARG58
B	ALA60
B	LYS95
B	SER103
B	GLY104
B	GLY105
B	ASP106
B	GLN107
B	TYR115
B	TRP157
B	GLY161
B	THR184
B	ASP185
B	VAL188
B	SER190
B	HOH542
B	HOH601
B	HOH608
B	HOH627
B	HOH637
B	HOH638
B	HOH648
B	HOH692
B	HOH699
B	HOH707
B	HOH737
B	HOH789
B	HOH817
E	PHE299
E	LYS302
E	HOH533
I	ALA14
I	LEU15

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PGE B 402

Chain	Residue
A	VAL204
B	ARG202
B	MET227
B	HOH683
C	GLN203

site_id	AC4
Number of Residues	29
Details	BINDING SITE FOR RESIDUE 2NE C 401

Chain	Residue
C	VAL57
C	ARG58
C	ALA60
C	SER103
C	GLY104
C	GLY105
C	ASP106
C	GLN107
C	TRP157
C	GLY160
C	GLY161
C	THR184
C	ASP185
C	SER190
C	HOH547
C	HOH625
C	HOH632
C	HOH643
C	HOH648
C	HOH652
C	HOH679
C	HOH683
C	HOH749
C	HOH819
D	PHE299
D	LYS302
D	HOH651
H	ALA14
H	LEU15

site_id	AC5
Number of Residues	24
Details	BINDING SITE FOR RESIDUE 2NE D 401

Chain	Residue
D	GLU56
D	VAL57
D	ARG58
D	ALA60
D	SER103
D	GLY104
D	GLY105
D	ASP106
D	GLN107
D	TYR115
D	TRP157
D	GLY161
D	THR184
D	ASP185
D	SER190
D	HOH614
D	HOH619
D	HOH647
D	HOH667
D	HOH697
A	SER119
C	TYR287
C	PHE299
C	LYS302

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PGE D 402

Chain	Residue
D	ARG202
D	GLN203
D	MET227
D	HOH515
D	HOH718
E	MET227

site_id	AC7
Number of Residues	34
Details	BINDING SITE FOR RESIDUE 2NE E 401

Chain	Residue
B	TYR287
B	PHE299
B	LYS302
B	HOH571
E	GLU56
E	VAL57
E	ARG58
E	ALA60
E	LYS95
E	SER103
E	GLY104
E	GLY105
E	ASP106
E	GLN107
E	TYR115
E	TRP157
E	GLY161
E	THR184
E	ASP185
E	VAL188
E	SER190
E	HOH530
E	HOH542
E	HOH621
E	HOH635
E	HOH703
E	HOH708
E	HOH709
E	HOH717
E	HOH740
E	HOH795
E	HOH808
E	HOH813
E	HOH819

site_id	AC8
Number of Residues	31
Details	BINDING SITE FOR RESIDUE 2NE F 401

Chain	Residue
A	TYR287
A	PHE299
A	LYS302
A	HOH678
F	GLU56
F	VAL57
F	ARG58
F	ALA60
F	LYS95
F	SER103
F	GLY104
F	GLY105
F	ASP106
F	GLN107
F	TYR115
F	TRP157
F	GLY161
F	THR184
F	ASP185
F	VAL188
F	SER190
F	HOH561
F	HOH563
F	HOH584
F	HOH617
F	HOH680
F	HOH723
F	HOH727
F	HOH751
F	HOH784
F	HOH796

site_id	AC9
Number of Residues	31
Details	BINDING SITE FOR RESIDUE 2NE G 401

Chain	Residue
A	LEU15
G	VAL57
G	ARG58
G	ALA60
G	LYS95
G	SER103
G	GLY104
G	GLY105
G	ASP106
G	GLN107
G	TYR115
G	TRP157
G	GLY161
G	THR184
G	ASP185
G	SER190
G	HOH536
G	HOH588
G	HOH599
G	HOH610
G	HOH635
G	HOH636
G	HOH656
G	HOH680
G	HOH707
G	HOH721
G	HOH726
L	PHE299
L	LYS302
L	HOH588
L	HOH774

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PGE G 402

Chain	Residue
G	ALA201
G	ARG202
G	GLN203
G	MET227
G	HOH629
H	HOH758
I	ARG202
I	VAL204
I	MET227

site_id	BC2
Number of Residues	34
Details	BINDING SITE FOR RESIDUE 2NE H 401

Chain	Residue
C	ALA14
C	LEU15
H	VAL57
H	ARG58
H	ALA60
H	LYS95
H	SER103
H	GLY104
H	GLY105
H	ASP106
H	GLN107
H	TYR115
H	LEU134
H	TRP157
H	GLY161
H	THR184
H	ASP185
H	SER190
H	HOH512
H	HOH540
H	HOH588
H	HOH633
H	HOH647
H	HOH665
H	HOH669
H	HOH692
H	HOH714
H	HOH751
H	HOH774
K	TYR287
K	PHE299
K	LYS302
K	HOH582
K	HOH721

site_id	BC3
Number of Residues	35
Details	BINDING SITE FOR RESIDUE 2NE I 401

Chain	Residue
B	ALA14
B	LEU15
I	VAL57
I	ARG58
I	ALA60
I	LYS95
I	SER103
I	GLY104
I	GLY105
I	ASP106
I	GLN107
I	TYR115
I	LEU134
I	TRP157
I	GLY161
I	THR184
I	ASP185
I	VAL188
I	SER190
I	HOH544
I	HOH573
I	HOH579
I	HOH651
I	HOH660
I	HOH673
I	HOH678
I	HOH725
I	HOH732
I	HOH777
I	HOH826
J	TYR287
J	PHE299
J	LYS302
J	HOH575
J	HOH602

site_id	BC4
Number of Residues	26
Details	BINDING SITE FOR RESIDUE 2NE J 401

Chain	Residue
I	PHE299
I	LYS302
I	HOH656
J	VAL57
J	ARG58
J	SER103
J	GLY104
J	GLY105
J	ASP106
J	GLN107
J	TYR115
J	TRP157
J	GLY161
J	THR184
J	ASP185
J	VAL188
J	SER190
J	HOH564
J	HOH627
J	HOH688
J	HOH692
J	HOH712
J	HOH720
J	HOH724
J	HOH743
J	HOH753

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PGE J 402

Chain	Residue
J	ARG202
J	HOH542
J	HOH623
J	HOH674
K	ARG202
L	ARG202

site_id	BC6
Number of Residues	28
Details	BINDING SITE FOR RESIDUE 2NE K 401

Chain	Residue
H	TYR287
H	PHE299
H	LYS302
H	HOH656
K	GLU56
K	VAL57
K	ARG58
K	ALA60
K	LYS95
K	SER103
K	GLY104
K	GLY105
K	ASP106
K	GLN107
K	TYR115
K	TRP157
K	GLY161
K	THR184
K	ASP185
K	VAL188
K	SER190
K	HOH572
K	HOH608
K	HOH621
K	HOH674
K	HOH675
K	HOH725
K	HOH741

site_id	BC7
Number of Residues	26
Details	BINDING SITE FOR RESIDUE 2NE L 401

Chain	Residue
G	TYR287
G	PHE299
G	LYS302
G	HOH683
L	GLU56
L	VAL57
L	ARG58
L	ALA60
L	LYS95
L	SER103
L	GLY104
L	GLY105
L	ASP106
L	GLN107
L	TYR115
L	TRP157
L	GLY161
L	THR184
L	ASP185
L	SER190
L	HOH572
L	HOH623
L	HOH636
L	HOH706
L	HOH778
L	HOH783

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12909628","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"12909628","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	48
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12909628","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16131752","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"UniProtKB","id":"P0ABU0","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	60
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12909628","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	12
Details	Binding site: {"description":"in other chain","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P0ABU0","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	12
Details	Site: {"description":"Important for catalysis","evidences":[{"source":"UniProtKB","id":"P0ABU0","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	12
Details	Site: {"description":"Important for catalysis","evidences":[{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"20643650","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"21830810","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	12
Details	Site: {"description":"Important for catalysis","evidences":[{"source":"UniProtKB","id":"P0ABU0","evidenceCode":"ECO:0000250"},{"source":"HAMAP-Rule","id":"MF_01934","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12909628","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
A	GLY105	electrostatic stabiliser, hydrogen bond donor
A	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
A	GLY161	electrostatic stabiliser, hydrogen bond donor
A	ASP185	activator
A	SER190	activator
A	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA10
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
J	GLY105	electrostatic stabiliser, hydrogen bond donor
J	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
J	GLY161	electrostatic stabiliser, hydrogen bond donor
J	ASP185	activator
J	SER190	activator
J	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA11
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
K	GLY105	electrostatic stabiliser, hydrogen bond donor
K	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
K	GLY161	electrostatic stabiliser, hydrogen bond donor
K	ASP185	activator
K	SER190	activator
K	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA12
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
L	GLY105	electrostatic stabiliser, hydrogen bond donor
L	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
L	GLY161	electrostatic stabiliser, hydrogen bond donor
L	ASP185	activator
L	SER190	activator
L	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA2
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
B	GLY105	electrostatic stabiliser, hydrogen bond donor
B	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
B	GLY161	electrostatic stabiliser, hydrogen bond donor
B	ASP185	activator
B	SER190	activator
B	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA3
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
C	GLY105	electrostatic stabiliser, hydrogen bond donor
C	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
C	GLY161	electrostatic stabiliser, hydrogen bond donor
C	ASP185	activator
C	SER190	activator
C	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA4
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
D	GLY105	electrostatic stabiliser, hydrogen bond donor
D	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
D	GLY161	electrostatic stabiliser, hydrogen bond donor
D	ASP185	activator
D	SER190	activator
D	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA5
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
E	GLY105	electrostatic stabiliser, hydrogen bond donor
E	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
E	GLY161	electrostatic stabiliser, hydrogen bond donor
E	ASP185	activator
E	SER190	activator
E	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA6
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
F	GLY105	electrostatic stabiliser, hydrogen bond donor
F	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
F	GLY161	electrostatic stabiliser, hydrogen bond donor
F	ASP185	activator
F	SER190	activator
F	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA7
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
G	GLY105	electrostatic stabiliser, hydrogen bond donor
G	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
G	GLY161	electrostatic stabiliser, hydrogen bond donor
G	ASP185	activator
G	SER190	activator
G	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA8
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
H	GLY105	electrostatic stabiliser, hydrogen bond donor
H	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
H	GLY161	electrostatic stabiliser, hydrogen bond donor
H	ASP185	activator
H	SER190	activator
H	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

site_id	MCSA9
Number of Residues	6
Details	M-CSA 346

Chain	Residue	Details
I	GLY105	electrostatic stabiliser, hydrogen bond donor
I	TYR115	electrostatic stabiliser, hydrogen bond donor, steric role
I	GLY161	electrostatic stabiliser, hydrogen bond donor
I	ASP185	activator
I	SER190	activator
I	TYR287	electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, steric role

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