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 | 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 | 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 | 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 | 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 | 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 | 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 | 6 |
Details | MOD_RES: N6-lipoyllysine => ECO:0000255|HAMAP-Rule:MF_00272 |
Chain | Residue | Details |
B | XOK602 | |
E | CYS60 | |
E | CYS66 | |
E | SER292 | |
G | CYS55 | |
G | CYS60 | |
G | CYS66 | |
G | SER292 | |
I | CYS55 | |
I | CYS60 | |
I | CYS66 | |
D | XOK602 | |
I | SER292 | |
K | CYS55 | |
K | CYS60 | |
K | CYS66 | |
K | SER292 | |
F | XOK602 | |
H | XOK602 | |
J | XOK602 | |
L | XOK602 | |
C | CYS66 | |
C | SER292 | |
E | CYS55 |
site_id | SWS_FT_FI2 |
Number of Residues | 18 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00206, ECO:0000269|PubMed:27506792, ECO:0007744|PDB:5EXI, ECO:0007744|PDB:5EXJ, ECO:0007744|PDB:5EXK |
Chain | Residue | Details |
A | CYS81 | |
G | CYS81 | |
G | CYS85 | |
G | CYS88 | |
I | CYS81 | |
I | CYS85 | |
I | CYS88 | |
K | CYS81 | |
K | CYS85 | |
K | CYS88 | |
A | CYS85 | |
A | CYS88 | |
C | CYS81 | |
C | CYS85 | |
C | CYS88 | |
E | CYS81 | |
E | CYS85 | |
E | CYS88 |