Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5EXK

Crystal structure of M. tuberculosis lipoyl synthase with 6-thiooctanoyl peptide intermediate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005737	cellular_component	cytoplasm
A	0009107	biological_process	lipoate biosynthetic process
A	0009249	biological_process	protein lipoylation
A	0016740	molecular_function	transferase activity
A	0016783	molecular_function	sulfurtransferase activity
A	0016992	molecular_function	lipoate synthase activity
A	0046872	molecular_function	metal ion binding
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0003824	molecular_function	catalytic activity
C	0005737	cellular_component	cytoplasm
C	0009107	biological_process	lipoate biosynthetic process
C	0009249	biological_process	protein lipoylation
C	0016740	molecular_function	transferase activity
C	0016783	molecular_function	sulfurtransferase activity
C	0016992	molecular_function	lipoate synthase activity
C	0046872	molecular_function	metal ion binding
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
E	0003824	molecular_function	catalytic activity
E	0005737	cellular_component	cytoplasm
E	0009107	biological_process	lipoate biosynthetic process
E	0009249	biological_process	protein lipoylation
E	0016740	molecular_function	transferase activity
E	0016783	molecular_function	sulfurtransferase activity
E	0016992	molecular_function	lipoate synthase activity
E	0046872	molecular_function	metal ion binding
E	0051536	molecular_function	iron-sulfur cluster binding
E	0051539	molecular_function	4 iron, 4 sulfur cluster binding
G	0003824	molecular_function	catalytic activity
G	0005737	cellular_component	cytoplasm
G	0009107	biological_process	lipoate biosynthetic process
G	0009249	biological_process	protein lipoylation
G	0016740	molecular_function	transferase activity
G	0016783	molecular_function	sulfurtransferase activity
G	0016992	molecular_function	lipoate synthase activity
G	0046872	molecular_function	metal ion binding
G	0051536	molecular_function	iron-sulfur cluster binding
G	0051539	molecular_function	4 iron, 4 sulfur cluster binding
I	0003824	molecular_function	catalytic activity
I	0005737	cellular_component	cytoplasm
I	0009107	biological_process	lipoate biosynthetic process
I	0009249	biological_process	protein lipoylation
I	0016740	molecular_function	transferase activity
I	0016783	molecular_function	sulfurtransferase activity
I	0016992	molecular_function	lipoate synthase activity
I	0046872	molecular_function	metal ion binding
I	0051536	molecular_function	iron-sulfur cluster binding
I	0051539	molecular_function	4 iron, 4 sulfur cluster binding
K	0003824	molecular_function	catalytic activity
K	0005737	cellular_component	cytoplasm
K	0009107	biological_process	lipoate biosynthetic process
K	0009249	biological_process	protein lipoylation
K	0016740	molecular_function	transferase activity
K	0016783	molecular_function	sulfurtransferase activity
K	0016992	molecular_function	lipoate synthase activity
K	0046872	molecular_function	metal ion binding
K	0051536	molecular_function	iron-sulfur cluster binding
K	0051539	molecular_function	4 iron, 4 sulfur cluster binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	binding site for residue F3S A 401

Chain	Residue
A	CYS55
A	CYS60
A	ASN62
A	ILE63
A	CYS66
A	THR73
A	ARG290
B	XOK602

site_id	AC2
Number of Residues	8
Details	binding site for residue SF4 A 402

Chain	Residue
A	ARG83
A	CYS85
A	PHE87
A	CYS88
A	ARG192
A	PHE195
A	MET404
A	CYS81

site_id	AC3
Number of Residues	15
Details	binding site for residue 5AD A 403

Chain	Residue
A	VAL54
A	PHE87
A	ASN180
A	GLU182
A	ASN217
A	ILE219
A	TYR249
A	LEU250
A	ARG290
A	MET404
A	HOH578
A	HOH593
A	HOH671
A	HOH675
B	XOK602

site_id	AC4
Number of Residues	10
Details	binding site for residue MET A 404

Chain	Residue
A	THR121
A	GLY122
A	ILE156
A	PRO157
A	ARG192
A	PHE195
A	SF4402
A	5AD403
A	HOH578
A	HOH678

site_id	AC5
Number of Residues	7
Details	binding site for residue IMD A 405

Chain	Residue
A	GLU14
A	ARG84
A	CYS85
A	ASP86
A	CYS88
A	ARG255
A	HIS256

site_id	AC6
Number of Residues	5
Details	binding site for residue CL A 406

Chain	Residue
A	PHE159
A	ARG165
A	HOH632
A	HOH664
K	ARG294

site_id	AC7
Number of Residues	8
Details	binding site for residue F3S C 401

Chain	Residue
C	CYS55
C	CYS60
C	ASN62
C	ILE63
C	CYS66
C	THR73
C	ARG290
D	XOK602

site_id	AC8
Number of Residues	8
Details	binding site for residue SF4 C 402

Chain	Residue
C	CYS81
C	ARG83
C	CYS85
C	PHE87
C	CYS88
C	ARG192
C	PHE195
C	MET404

site_id	AC9
Number of Residues	14
Details	binding site for residue 5AD C 403

Chain	Residue
C	VAL54
C	PHE87
C	ASN180
C	GLU182
C	ASN217
C	TYR249
C	LEU250
C	ARG290
C	MET404
C	HOH548
C	HOH611
C	HOH659
C	HOH666
D	XOK602

site_id	AD1
Number of Residues	10
Details	binding site for residue MET C 404

Chain	Residue
C	THR121
C	GLY122
C	ILE156
C	PRO157
C	ARG192
C	PHE195
C	SF4402
C	5AD403
C	HOH548
C	HOH661

site_id	AD2
Number of Residues	3
Details	binding site for residue IPA C 405

Chain	Residue
C	ARG141
C	GLU171
C	SER172

site_id	AD3
Number of Residues	8
Details	binding site for residue F3S E 401

Chain	Residue
E	ILE63
E	CYS66
E	THR73
E	ARG290
F	XOK602
E	CYS55
E	CYS60
E	ASN62

site_id	AD4
Number of Residues	7
Details	binding site for residue SF4 E 402

Chain	Residue
E	CYS81
E	ARG83
E	CYS85
E	CYS88
E	ARG192
E	PHE195
E	MET404

site_id	AD5
Number of Residues	14
Details	binding site for residue 5AD E 403

Chain	Residue
E	VAL54
E	PHE87
E	ASN180
E	GLU182
E	ASN217
E	TYR249
E	LEU250
E	ARG290
E	MET404
E	HOH576
E	HOH626
E	HOH641
E	HOH656
F	XOK602

site_id	AD6
Number of Residues	10
Details	binding site for residue MET E 404

Chain	Residue
E	THR121
E	GLY122
E	ILE156
E	PRO157
E	ARG192
E	PHE195
E	SF4402
E	5AD403
E	HOH576
E	HOH677

site_id	AD7
Number of Residues	8
Details	binding site for residue IMD E 405

Chain	Residue
E	GLU14
E	ARG84
E	CYS85
E	ASP86
E	CYS88
E	ARG255
E	HIS256
E	HOH631

site_id	AD8
Number of Residues	8
Details	binding site for residue F3S G 401

Chain	Residue
G	CYS55
G	CYS60
G	ILE63
G	CYS66
G	THR73
G	ARG290
G	HOH724
H	XOK602

site_id	AD9
Number of Residues	8
Details	binding site for residue SF4 G 402

Chain	Residue
G	CYS81
G	ARG83
G	CYS85
G	PHE87
G	CYS88
G	ARG192
G	PHE195
G	MET404

site_id	AE1
Number of Residues	16
Details	binding site for residue 5AD G 403

Chain	Residue
G	VAL54
G	PHE87
G	LEU155
G	ASN180
G	GLU182
G	ASN217
G	ILE219
G	TYR249
G	LEU250
G	PRO252
G	ARG290
G	MET404
G	HOH555
G	HOH577
G	HOH616
H	XOK602

site_id	AE2
Number of Residues	10
Details	binding site for residue MET G 404

Chain	Residue
G	THR121
G	GLY122
G	ILE156
G	PRO157
G	ARG192
G	PHE195
G	SF4402
G	5AD403
G	HOH577
G	HOH648

site_id	AE3
Number of Residues	8
Details	binding site for residue F3S I 401

Chain	Residue
I	CYS55
I	CYS60
I	ASN62
I	ILE63
I	CYS66
I	THR73
I	ARG290
J	XOK602

site_id	AE4
Number of Residues	8
Details	binding site for residue SF4 I 402

Chain	Residue
I	CYS81
I	ARG83
I	CYS85
I	PHE87
I	CYS88
I	ARG192
I	PHE195
I	MET404

site_id	AE5
Number of Residues	14
Details	binding site for residue 5AD I 403

Chain	Residue
I	VAL54
I	PHE87
I	ASN180
I	GLU182
I	ASN217
I	TYR249
I	LEU250
I	ARG290
I	MET404
I	HOH549
I	HOH605
I	HOH647
I	HOH651
J	XOK602

site_id	AE6
Number of Residues	10
Details	binding site for residue MET I 404

Chain	Residue
I	THR121
I	GLY122
I	ILE156
I	PRO157
I	ARG192
I	PHE195
I	SF4402
I	5AD403
I	HOH549
I	HOH623

site_id	AE7
Number of Residues	9
Details	binding site for residue F3S K 401

Chain	Residue
K	CYS55
K	CYS60
K	ASN62
K	ILE63
K	CYS66
K	THR73
K	ARG290
K	TYR293
L	XOK602

site_id	AE8
Number of Residues	7
Details	binding site for residue SF4 K 402

Chain	Residue
K	CYS81
K	ARG83
K	CYS85
K	CYS88
K	ARG192
K	PHE195
K	MET404

site_id	AE9
Number of Residues	15
Details	binding site for residue 5AD K 403

Chain	Residue
K	VAL54
K	PHE87
K	ASN180
K	GLU182
K	ASN217
K	ILE219
K	TYR249
K	LEU250
K	ARG290
K	MET404
K	HOH532
K	HOH609
K	HOH638
K	HOH659
L	XOK602

site_id	AF1
Number of Residues	10
Details	binding site for residue MET K 404

Chain	Residue
K	THR121
K	GLY122
K	ILE156
K	PRO157
K	ARG192
K	PHE195
K	SF4402
K	5AD403
K	HOH532
K	HOH628

site_id	AF2
Number of Residues	3
Details	binding site for residue CL K 405

Chain	Residue
K	PHE159
K	ARG165
K	HOH550

site_id	AF3
Number of Residues	14
Details	binding site for Ligand residues XOK B 602 through SER B 603 bound to THR B 601

Chain	Residue
A	VAL54
A	CYS55
A	ALA58
A	GLY59
A	CYS60
A	LEU250
A	ARG290
A	SER292
A	F3S401
A	5AD403
A	HOH674
B	THR601
B	VAL604
B	HOH702

site_id	AF4
Number of Residues	15
Details	binding site for Ligand residues XOK D 602 through SER D 603 bound to THR D 601

Chain	Residue
C	LYS25
C	CYS55
C	ALA58
C	GLY59
C	CYS60
C	LEU250
C	ARG290
C	SER292
C	F3S401
C	5AD403
D	THR601
D	VAL604
D	HOH702
D	HOH706
D	HOH707

site_id	AF5
Number of Residues	15
Details	binding site for Ligand residues XOK F 602 through SER F 603 bound to THR F 601

Chain	Residue
E	LYS25
E	VAL54
E	CYS55
E	ALA58
E	GLY59
E	CYS60
E	LEU250
E	ARG290
E	SER292
E	F3S401
E	5AD403
E	HOH639
F	THR601
F	VAL604
F	HOH702

site_id	AF6
Number of Residues	15
Details	binding site for Ligand residues XOK H 602 through SER H 603 bound to THR H 601

Chain	Residue
G	LYS25
G	VAL54
G	CYS55
G	ALA58
G	GLY59
G	CYS60
G	LEU250
G	ARG290
G	SER291
G	SER292
G	F3S401
G	5AD403
H	THR601
H	VAL604
H	HOH702

site_id	AF7
Number of Residues	15
Details	binding site for Ligand residues XOK J 602 through SER J 603 bound to THR J 601

Chain	Residue
I	LYS25
I	VAL54
I	CYS55
I	ALA58
I	GLY59
I	CYS60
I	ARG251
I	ARG290
I	SER292
I	F3S401
I	5AD403
J	THR601
J	VAL604
J	HOH701
J	HOH702

site_id	AF8
Number of Residues	16
Details	binding site for Ligand residues XOK L 602 through SER L 603 bound to THR L 601

Chain	Residue
K	VAL54
K	CYS55
K	ALA58
K	GLY59
K	CYS60
K	LEU250
K	ARG290
K	SER292
K	F3S401
K	5AD403
K	HOH626
L	SER600
L	THR601
L	VAL604
L	HOH701
L	HOH703

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1284
Details	Domain: {"description":"Radical SAM core","evidences":[{"source":"PROSITE-ProRule","id":"PRU01266","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00206","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"27506792","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5EXI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5EXJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00206","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"27506792","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"5EXI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5EXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5EXK","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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