2AF6
Crystal structure of Mycobacterium tuberculosis Flavin dependent thymidylate synthase (Mtb ThyX) in the presence of co-factor FAD and substrate analog 5-Bromo-2'-Deoxyuridine-5'-Monophosphate (BrdUMP)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004799 | molecular_function | thymidylate synthase activity |
| A | 0006231 | biological_process | dTMP biosynthetic process |
| A | 0006235 | biological_process | dTTP biosynthetic process |
| A | 0008168 | molecular_function | methyltransferase activity |
| A | 0009165 | biological_process | nucleotide biosynthetic process |
| A | 0016740 | molecular_function | transferase activity |
| A | 0032259 | biological_process | methylation |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| A | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| A | 0070402 | molecular_function | NADPH binding |
| B | 0004799 | molecular_function | thymidylate synthase activity |
| B | 0006231 | biological_process | dTMP biosynthetic process |
| B | 0006235 | biological_process | dTTP biosynthetic process |
| B | 0008168 | molecular_function | methyltransferase activity |
| B | 0009165 | biological_process | nucleotide biosynthetic process |
| B | 0016740 | molecular_function | transferase activity |
| B | 0032259 | biological_process | methylation |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| B | 0070402 | molecular_function | NADPH binding |
| C | 0004799 | molecular_function | thymidylate synthase activity |
| C | 0006231 | biological_process | dTMP biosynthetic process |
| C | 0006235 | biological_process | dTTP biosynthetic process |
| C | 0008168 | molecular_function | methyltransferase activity |
| C | 0009165 | biological_process | nucleotide biosynthetic process |
| C | 0016740 | molecular_function | transferase activity |
| C | 0032259 | biological_process | methylation |
| C | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| C | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| C | 0070402 | molecular_function | NADPH binding |
| D | 0004799 | molecular_function | thymidylate synthase activity |
| D | 0006231 | biological_process | dTMP biosynthetic process |
| D | 0006235 | biological_process | dTTP biosynthetic process |
| D | 0008168 | molecular_function | methyltransferase activity |
| D | 0009165 | biological_process | nucleotide biosynthetic process |
| D | 0016740 | molecular_function | transferase activity |
| D | 0032259 | biological_process | methylation |
| D | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| D | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| D | 0070402 | molecular_function | NADPH binding |
| E | 0004799 | molecular_function | thymidylate synthase activity |
| E | 0006231 | biological_process | dTMP biosynthetic process |
| E | 0006235 | biological_process | dTTP biosynthetic process |
| E | 0008168 | molecular_function | methyltransferase activity |
| E | 0009165 | biological_process | nucleotide biosynthetic process |
| E | 0016740 | molecular_function | transferase activity |
| E | 0032259 | biological_process | methylation |
| E | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| E | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| E | 0070402 | molecular_function | NADPH binding |
| F | 0004799 | molecular_function | thymidylate synthase activity |
| F | 0006231 | biological_process | dTMP biosynthetic process |
| F | 0006235 | biological_process | dTTP biosynthetic process |
| F | 0008168 | molecular_function | methyltransferase activity |
| F | 0009165 | biological_process | nucleotide biosynthetic process |
| F | 0016740 | molecular_function | transferase activity |
| F | 0032259 | biological_process | methylation |
| F | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| F | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| F | 0070402 | molecular_function | NADPH binding |
| G | 0004799 | molecular_function | thymidylate synthase activity |
| G | 0006231 | biological_process | dTMP biosynthetic process |
| G | 0006235 | biological_process | dTTP biosynthetic process |
| G | 0008168 | molecular_function | methyltransferase activity |
| G | 0009165 | biological_process | nucleotide biosynthetic process |
| G | 0016740 | molecular_function | transferase activity |
| G | 0032259 | biological_process | methylation |
| G | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| G | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| G | 0070402 | molecular_function | NADPH binding |
| H | 0004799 | molecular_function | thymidylate synthase activity |
| H | 0006231 | biological_process | dTMP biosynthetic process |
| H | 0006235 | biological_process | dTTP biosynthetic process |
| H | 0008168 | molecular_function | methyltransferase activity |
| H | 0009165 | biological_process | nucleotide biosynthetic process |
| H | 0016740 | molecular_function | transferase activity |
| H | 0032259 | biological_process | methylation |
| H | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| H | 0050797 | molecular_function | thymidylate synthase (FAD) activity |
| H | 0070402 | molecular_function | NADPH binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE IOD A 3001 |
| Chain | Residue |
| A | ALA247 |
| A | HOH4737 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE IOD D 3002 |
| Chain | Residue |
| C | FAD2600 |
| D | PHE70 |
| D | SER71 |
| D | GOL2012 |
| site_id | AC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE IOD G 3003 |
| Chain | Residue |
| G | THR54 |
| G | HOH6715 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE IOD D 3004 |
| Chain | Residue |
| D | VAL222 |
| D | HOH3122 |
| D | HOH3123 |
| D | HOH3124 |
| D | TYR189 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE IOD F 3005 |
| Chain | Residue |
| F | LYS14 |
| F | THR15 |
| F | GLY32 |
| F | TYR189 |
| F | VAL222 |
| F | HOH7704 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE IOD E 3006 |
| Chain | Residue |
| E | VAL23 |
| G | GLN10 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE IOD E 3007 |
| Chain | Residue |
| E | THR4 |
| site_id | AC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE IOD A 3008 |
| Chain | Residue |
| A | THR4 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE IOD C 3009 |
| Chain | Residue |
| C | THR4 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE IOD F 3010 |
| Chain | Residue |
| F | ARG41 |
| F | PRO50 |
| F | THR54 |
| F | GOL2014 |
| F | HOH7707 |
| site_id | BC2 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE FAD D 1600 |
| Chain | Residue |
| A | SER102 |
| A | GLN103 |
| A | SER105 |
| C | CYS43 |
| C | SER71 |
| C | GLU74 |
| C | HIS98 |
| C | ASN188 |
| C | ARG190 |
| C | FAD2600 |
| D | ARG95 |
| D | HIS96 |
| D | ARG97 |
| D | HIS98 |
| D | HIS194 |
| D | MSE198 |
| D | ARG199 |
| D | HIS203 |
| D | BRU1603 |
| D | HOH3026 |
| D | HOH3040 |
| D | HOH3050 |
| D | HOH3054 |
| site_id | BC3 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE BRU D 1603 |
| Chain | Residue |
| A | ARG87 |
| A | GLN103 |
| A | LEU104 |
| A | SER105 |
| A | GLN106 |
| A | ARG107 |
| A | ARG172 |
| D | HIS91 |
| D | GLU92 |
| D | ARG95 |
| D | ARG199 |
| D | FAD1600 |
| D | HOH3014 |
| D | HOH3019 |
| site_id | BC4 |
| Number of Residues | 26 |
| Details | BINDING SITE FOR RESIDUE FAD C 2600 |
| Chain | Residue |
| B | SER102 |
| B | GLN103 |
| B | SER105 |
| B | HOH3689 |
| C | ARG95 |
| C | HIS96 |
| C | ARG97 |
| C | HIS98 |
| C | HIS194 |
| C | MSE198 |
| C | ARG199 |
| C | HIS203 |
| C | BRU2603 |
| C | HOH3060 |
| C | HOH3074 |
| C | HOH3076 |
| C | HOH3078 |
| D | CYS43 |
| D | SER71 |
| D | GLU74 |
| D | HIS98 |
| D | ASN188 |
| D | ARG190 |
| D | FAD1600 |
| D | GOL2012 |
| D | IOD3002 |
| site_id | BC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU C 2603 |
| Chain | Residue |
| B | ARG172 |
| C | HIS91 |
| C | GLU92 |
| C | ARG95 |
| C | ARG199 |
| C | FAD2600 |
| C | HOH3015 |
| C | HOH3021 |
| B | ARG87 |
| B | GLN103 |
| B | LEU104 |
| B | SER105 |
| B | GLN106 |
| B | ARG107 |
| B | TYR108 |
| site_id | BC6 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE FAD B 3600 |
| Chain | Residue |
| A | CYS43 |
| A | SER71 |
| A | GLU74 |
| A | HIS98 |
| A | ASN188 |
| A | ARG190 |
| A | GOL2013 |
| A | FAD4600 |
| B | ARG95 |
| B | HIS96 |
| B | ARG97 |
| B | HIS98 |
| B | HIS194 |
| B | MSE198 |
| B | ARG199 |
| B | HIS203 |
| B | BRU3603 |
| B | HOH3647 |
| B | HOH3660 |
| B | HOH3723 |
| C | SER102 |
| C | GLN103 |
| C | SER105 |
| C | TYR108 |
| C | HOH3073 |
| site_id | BC7 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU B 3603 |
| Chain | Residue |
| B | HIS91 |
| B | GLU92 |
| B | ARG95 |
| B | ARG199 |
| B | FAD3600 |
| B | HOH3604 |
| B | HOH3615 |
| C | ARG87 |
| C | GLN103 |
| C | LEU104 |
| C | SER105 |
| C | GLN106 |
| C | ARG107 |
| C | TYR108 |
| C | ARG172 |
| site_id | BC8 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE FAD A 4600 |
| Chain | Residue |
| A | ARG95 |
| A | HIS96 |
| A | ARG97 |
| A | HIS98 |
| A | HIS194 |
| A | MSE198 |
| A | ARG199 |
| A | HIS203 |
| A | BRU4603 |
| A | HOH4627 |
| A | HOH4636 |
| A | HOH4647 |
| A | HOH4701 |
| A | HOH4726 |
| A | HOH4731 |
| B | CYS43 |
| B | SER71 |
| B | GLU74 |
| B | HIS98 |
| B | ASN188 |
| B | ARG190 |
| B | FAD3600 |
| D | SER102 |
| D | GLN103 |
| D | TYR108 |
| site_id | BC9 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU A 4603 |
| Chain | Residue |
| A | HIS91 |
| A | GLU92 |
| A | ARG95 |
| A | ARG199 |
| A | FAD4600 |
| A | HOH4606 |
| A | HOH4634 |
| D | ARG87 |
| D | GLN103 |
| D | LEU104 |
| D | SER105 |
| D | GLN106 |
| D | ARG107 |
| D | TYR108 |
| D | ARG172 |
| site_id | CC1 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE FAD H 5600 |
| Chain | Residue |
| E | SER102 |
| E | GLN103 |
| E | TYR108 |
| E | HOH8648 |
| E | HOH8676 |
| G | CYS43 |
| G | SER71 |
| G | HIS98 |
| G | ASN188 |
| G | ARG190 |
| G | FAD6600 |
| H | ARG95 |
| H | HIS96 |
| H | ARG97 |
| H | HIS98 |
| H | HIS194 |
| H | MSE198 |
| H | ARG199 |
| H | HIS203 |
| H | BRU5603 |
| H | HOH5664 |
| H | HOH5670 |
| H | HOH5689 |
| site_id | CC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU H 5603 |
| Chain | Residue |
| E | ARG87 |
| E | GLN103 |
| E | LEU104 |
| E | SER105 |
| E | GLN106 |
| E | ARG107 |
| E | TYR108 |
| E | ARG172 |
| H | HIS91 |
| H | GLU92 |
| H | ARG95 |
| H | ARG199 |
| H | FAD5600 |
| H | HOH5606 |
| H | HOH5614 |
| site_id | CC3 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE FAD G 6600 |
| Chain | Residue |
| F | SER102 |
| F | GLN103 |
| F | SER105 |
| F | HOH7634 |
| F | HOH7690 |
| G | ARG95 |
| G | HIS96 |
| G | ARG97 |
| G | HIS98 |
| G | HIS194 |
| G | MSE198 |
| G | ARG199 |
| G | BRU6603 |
| G | HOH6656 |
| G | HOH6658 |
| H | CYS43 |
| H | SER71 |
| H | GLU74 |
| H | HIS98 |
| H | ASN188 |
| H | ARG190 |
| H | FAD5600 |
| site_id | CC4 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU G 6603 |
| Chain | Residue |
| F | ARG87 |
| F | GLN103 |
| F | LEU104 |
| F | SER105 |
| F | GLN106 |
| F | ARG107 |
| F | TYR108 |
| F | ARG172 |
| G | HIS91 |
| G | GLU92 |
| G | ARG95 |
| G | ARG199 |
| G | FAD6600 |
| G | HOH6607 |
| G | HOH6624 |
| site_id | CC5 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE FAD F 7600 |
| Chain | Residue |
| E | CYS43 |
| E | SER71 |
| E | GLU74 |
| E | HIS98 |
| E | ASN188 |
| E | ARG190 |
| E | FAD8600 |
| F | ARG95 |
| F | HIS96 |
| F | ARG97 |
| F | HIS98 |
| F | HIS194 |
| F | MSE198 |
| F | ARG199 |
| F | HIS203 |
| F | BRU7603 |
| F | HOH7624 |
| F | HOH7653 |
| F | HOH7659 |
| F | HOH7696 |
| G | SER102 |
| G | GLN103 |
| G | SER105 |
| G | TYR108 |
| G | HOH6706 |
| site_id | CC6 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU F 7603 |
| Chain | Residue |
| F | HIS91 |
| F | GLU92 |
| F | ARG95 |
| F | ARG199 |
| F | FAD7600 |
| F | HOH7606 |
| F | HOH7613 |
| G | ARG87 |
| G | GLN103 |
| G | LEU104 |
| G | SER105 |
| G | GLN106 |
| G | ARG107 |
| G | TYR108 |
| G | ARG172 |
| site_id | CC7 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE FAD E 8600 |
| Chain | Residue |
| E | ARG95 |
| E | HIS96 |
| E | ARG97 |
| E | HIS98 |
| E | HIS194 |
| E | MSE198 |
| E | ARG199 |
| E | HIS203 |
| E | BRU8603 |
| E | HOH8661 |
| E | HOH8666 |
| E | HOH8688 |
| F | CYS43 |
| F | SER71 |
| F | GLU74 |
| F | HIS98 |
| F | ASN188 |
| F | ARG190 |
| F | GOL2007 |
| F | FAD7600 |
| H | SER102 |
| H | GLN103 |
| H | SER105 |
| site_id | CC8 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE BRU E 8603 |
| Chain | Residue |
| E | HIS91 |
| E | GLU92 |
| E | ARG95 |
| E | ARG199 |
| E | FAD8600 |
| E | HOH8604 |
| E | HOH8605 |
| H | ARG87 |
| H | GLN103 |
| H | LEU104 |
| H | SER105 |
| H | GLN106 |
| H | ARG107 |
| H | TYR108 |
| H | ARG172 |
| site_id | CC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 2001 |
| Chain | Residue |
| A | LYS14 |
| A | THR15 |
| A | GLY32 |
| A | SER77 |
| A | VAL78 |
| A | TYR189 |
| A | HOH4702 |
| site_id | DC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 2002 |
| Chain | Residue |
| B | LYS14 |
| B | THR15 |
| B | GLY31 |
| B | GLY32 |
| B | SER77 |
| B | VAL78 |
| B | TYR189 |
| B | VAL222 |
| site_id | DC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL C 2003 |
| Chain | Residue |
| C | LYS14 |
| C | THR15 |
| C | GLY31 |
| C | GLY32 |
| C | SER77 |
| C | VAL78 |
| C | TYR189 |
| C | VAL222 |
| C | HOH3093 |
| site_id | DC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL E 2004 |
| Chain | Residue |
| E | LYS14 |
| E | THR15 |
| E | GLY31 |
| E | GLY32 |
| E | SER77 |
| E | VAL78 |
| E | TYR189 |
| E | VAL222 |
| site_id | DC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL G 2005 |
| Chain | Residue |
| G | LYS14 |
| G | THR15 |
| G | GLY32 |
| G | SER77 |
| G | VAL78 |
| G | TYR189 |
| G | VAL222 |
| G | HOH6691 |
| site_id | DC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL H 2006 |
| Chain | Residue |
| H | LYS14 |
| H | THR15 |
| H | GLY31 |
| H | GLY32 |
| H | SER77 |
| H | TYR189 |
| H | VAL222 |
| H | HOH5605 |
| site_id | DC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL F 2007 |
| Chain | Residue |
| E | FAD8600 |
| F | HIS69 |
| F | SER71 |
| F | HOH7689 |
| site_id | DC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 2008 |
| Chain | Residue |
| B | LEU216 |
| B | ARG217 |
| B | PHE227 |
| B | PHE230 |
| B | HOH3617 |
| B | HOH3645 |
| F | SER48 |
| F | LYS49 |
| F | PRO50 |
| site_id | DC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL D 2009 |
| Chain | Residue |
| D | ARG41 |
| D | PRO50 |
| D | THR54 |
| D | TYR60 |
| site_id | DC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 2010 |
| Chain | Residue |
| A | ARG41 |
| A | THR54 |
| A | TYR60 |
| site_id | EC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL E 2011 |
| Chain | Residue |
| E | ARG87 |
| E | HIS91 |
| E | ASN177 |
| H | ARG87 |
| H | SER88 |
| H | HIS91 |
| H | ASN177 |
| site_id | EC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL D 2012 |
| Chain | Residue |
| C | FAD2600 |
| D | HIS69 |
| D | SER71 |
| D | VAL72 |
| D | IOD3002 |
| D | HOH3025 |
| D | HOH3117 |
| site_id | EC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 2013 |
| Chain | Residue |
| A | HIS69 |
| A | SER71 |
| A | VAL72 |
| A | HOH4619 |
| A | HOH4727 |
| B | FAD3600 |
| site_id | EC4 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL F 2014 |
| Chain | Residue |
| F | ARG41 |
| F | PRO50 |
| F | THR54 |
| F | IOD3010 |
| F | HOH7645 |
| F | HOH7706 |
| F | HOH7707 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 80 |
| Details | Motif: {"description":"ThyX motif","evidences":[{"source":"HAMAP-Rule","id":"MF_01408","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Active site: {"description":"Involved in ionization of N3 of dUMP, leading to its activation","evidences":[{"source":"HAMAP-Rule","id":"MF_01408","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 56 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16139296","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2AF6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3GWC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HZG","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 32 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"16139296","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2AF6","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 48 |
| Details | Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"16139296","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"2AF6","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
