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 |
