6SMN
A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with methotrexate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0006544 | biological_process | glycine metabolic process |
| A | 0006563 | biological_process | L-serine metabolic process |
| A | 0006730 | biological_process | one-carbon metabolic process |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0009507 | cellular_component | chloroplast |
| A | 0009536 | cellular_component | plastid |
| A | 0016740 | molecular_function | transferase activity |
| A | 0019264 | biological_process | glycine biosynthetic process from L-serine |
| A | 0030170 | molecular_function | pyridoxal phosphate binding |
| A | 0035999 | biological_process | tetrahydrofolate interconversion |
| A | 0045271 | cellular_component | respiratory chain complex I |
| A | 0046653 | biological_process | tetrahydrofolate metabolic process |
| A | 0050897 | molecular_function | cobalt ion binding |
| B | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0006544 | biological_process | glycine metabolic process |
| B | 0006563 | biological_process | L-serine metabolic process |
| B | 0006730 | biological_process | one-carbon metabolic process |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0009507 | cellular_component | chloroplast |
| B | 0009536 | cellular_component | plastid |
| B | 0016740 | molecular_function | transferase activity |
| B | 0019264 | biological_process | glycine biosynthetic process from L-serine |
| B | 0030170 | molecular_function | pyridoxal phosphate binding |
| B | 0035999 | biological_process | tetrahydrofolate interconversion |
| B | 0045271 | cellular_component | respiratory chain complex I |
| B | 0046653 | biological_process | tetrahydrofolate metabolic process |
| B | 0050897 | molecular_function | cobalt ion binding |
| C | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0006544 | biological_process | glycine metabolic process |
| C | 0006563 | biological_process | L-serine metabolic process |
| C | 0006730 | biological_process | one-carbon metabolic process |
| C | 0008270 | molecular_function | zinc ion binding |
| C | 0009507 | cellular_component | chloroplast |
| C | 0009536 | cellular_component | plastid |
| C | 0016740 | molecular_function | transferase activity |
| C | 0019264 | biological_process | glycine biosynthetic process from L-serine |
| C | 0030170 | molecular_function | pyridoxal phosphate binding |
| C | 0035999 | biological_process | tetrahydrofolate interconversion |
| C | 0045271 | cellular_component | respiratory chain complex I |
| C | 0046653 | biological_process | tetrahydrofolate metabolic process |
| C | 0050897 | molecular_function | cobalt ion binding |
| D | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0006544 | biological_process | glycine metabolic process |
| D | 0006563 | biological_process | L-serine metabolic process |
| D | 0006730 | biological_process | one-carbon metabolic process |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0009507 | cellular_component | chloroplast |
| D | 0009536 | cellular_component | plastid |
| D | 0016740 | molecular_function | transferase activity |
| D | 0019264 | biological_process | glycine biosynthetic process from L-serine |
| D | 0030170 | molecular_function | pyridoxal phosphate binding |
| D | 0035999 | biological_process | tetrahydrofolate interconversion |
| D | 0045271 | cellular_component | respiratory chain complex I |
| D | 0046653 | biological_process | tetrahydrofolate metabolic process |
| D | 0050897 | molecular_function | cobalt ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 21 |
| Details | binding site for residue PLS A 601 |
| Chain | Residue |
| A | SER82 |
| A | HIS260 |
| A | THR283 |
| A | HIS285 |
| A | LYS286 |
| A | ARG430 |
| A | HOH773 |
| B | TYR102 |
| B | GLU104 |
| B | TYR112 |
| B | GLY330 |
| A | SER148 |
| B | GLY331 |
| B | HOH2677 |
| A | GLY149 |
| A | SER150 |
| A | HIS177 |
| A | ALA231 |
| A | SER232 |
| A | ASP257 |
| A | ALA259 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 602 |
| Chain | Residue |
| A | ALA169 |
| A | ASP171 |
| A | HIS180 |
| A | GLY181 |
| A | THR198 |
| A | MET199 |
| site_id | AC3 |
| Number of Residues | 17 |
| Details | binding site for residue MTX A 603 |
| Chain | Residue |
| A | TYR182 |
| A | THR184 |
| A | THR186 |
| A | ILE189 |
| A | ASN413 |
| A | LYS414 |
| A | ALA423 |
| A | EDO605 |
| A | EDO615 |
| A | HOH829 |
| A | HOH916 |
| A | HOH1007 |
| A | HOH1028 |
| B | GLU104 |
| B | TYR111 |
| B | PHE325 |
| B | HOH2704 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 604 |
| Chain | Residue |
| A | GLN126 |
| A | LEU130 |
| A | GLY141 |
| A | VAL142 |
| A | HOH728 |
| A | HOH793 |
| A | HOH841 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 605 |
| Chain | Residue |
| A | LEU172 |
| A | GLY176 |
| A | HIS177 |
| A | LEU178 |
| A | SER232 |
| A | MTX603 |
| A | HOH851 |
| B | HOH2531 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 606 |
| Chain | Residue |
| A | PRO151 |
| A | PHE154 |
| A | HOH714 |
| A | HOH736 |
| A | HOH753 |
| A | HOH1054 |
| B | PRO151 |
| B | PHE154 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 607 |
| Chain | Residue |
| A | PRO504 |
| A | THR505 |
| A | GLU509 |
| A | EDO610 |
| A | HOH820 |
| A | HOH822 |
| B | ASN52 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 608 |
| Chain | Residue |
| A | ALA159 |
| A | LEU160 |
| A | LEU161 |
| A | LYS162 |
| A | ARG319 |
| A | HOH885 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 609 |
| Chain | Residue |
| A | GLU61 |
| A | ASP64 |
| A | HOH718 |
| A | HOH948 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 610 |
| Chain | Residue |
| A | GLU509 |
| A | LYS510 |
| A | GLU511 |
| A | EDO607 |
| A | HOH820 |
| D | LYS307 |
| D | GLY309 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 611 |
| Chain | Residue |
| A | ARG110 |
| A | TYR111 |
| B | LYS414 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 612 |
| Chain | Residue |
| A | HOH962 |
| A | ILE210 |
| A | ASP211 |
| A | TYR212 |
| A | ASP213 |
| A | HOH732 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 613 |
| Chain | Residue |
| A | ARG348 |
| A | PRO350 |
| A | LYS353 |
| A | HOH716 |
| site_id | AD5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 614 |
| Chain | Residue |
| A | LEU55 |
| A | ASP56 |
| A | ALA63 |
| A | GLU67 |
| A | HOH845 |
| A | HOH934 |
| site_id | AD6 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 615 |
| Chain | Residue |
| A | MET424 |
| A | MTX603 |
| A | HOH918 |
| B | TYR111 |
| site_id | AD7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 616 |
| Chain | Residue |
| A | LYS414 |
| B | ALA109 |
| B | ARG110 |
| site_id | AD8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 617 |
| Chain | Residue |
| A | LYS188 |
| A | ILE189 |
| B | GLN322 |
| B | HOH2719 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 2401 |
| Chain | Residue |
| A | GLN322 |
| A | HOH959 |
| B | LYS188 |
| B | ILE189 |
| site_id | AE1 |
| Number of Residues | 22 |
| Details | binding site for residue PLS B 2402 |
| Chain | Residue |
| A | TYR102 |
| A | GLU104 |
| A | TYR112 |
| A | GLY330 |
| A | GLY331 |
| A | HOH897 |
| B | SER82 |
| B | SER148 |
| B | GLY149 |
| B | SER150 |
| B | HIS177 |
| B | ALA231 |
| B | SER232 |
| B | ASP257 |
| B | ALA259 |
| B | HIS260 |
| B | THR283 |
| B | HIS285 |
| B | LYS286 |
| B | ARG430 |
| B | HOH2602 |
| B | HOH2810 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 2403 |
| Chain | Residue |
| B | LEU170 |
| B | HIS180 |
| B | GLY181 |
| B | THR198 |
| B | MET199 |
| B | PRO200 |
| site_id | AE3 |
| Number of Residues | 10 |
| Details | binding site for residue MTX B 2404 |
| Chain | Residue |
| A | GLU104 |
| A | TYR111 |
| B | TYR182 |
| B | THR184 |
| B | ASP185 |
| B | THR186 |
| B | ASN413 |
| B | LYS414 |
| B | HOH2638 |
| B | HOH2778 |
| site_id | AE4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 2405 |
| Chain | Residue |
| B | GLN126 |
| B | LEU130 |
| B | GLY141 |
| B | VAL142 |
| B | HOH2542 |
| B | HOH2559 |
| B | HOH2633 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 2406 |
| Chain | Residue |
| B | TYR375 |
| B | LYS394 |
| B | ASP454 |
| B | LYS458 |
| B | HOH2746 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 2407 |
| Chain | Residue |
| A | MET120 |
| B | ASP64 |
| B | ILE65 |
| B | LEU68 |
| B | HOH2729 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 2408 |
| Chain | Residue |
| B | TRP140 |
| B | PHE274 |
| B | HOH2723 |
| site_id | AE8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 2409 |
| Chain | Residue |
| B | ALA159 |
| B | LEU160 |
| B | LEU161 |
| B | LYS162 |
| B | ARG319 |
| B | HOH2613 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 2410 |
| Chain | Residue |
| B | ASP211 |
| B | TYR212 |
| B | ASP213 |
| B | HOH2502 |
| B | HOH2538 |
| site_id | AF1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 2411 |
| Chain | Residue |
| B | GLN134 |
| B | LEU135 |
| B | ASP136 |
| site_id | AF2 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 2412 |
| Chain | Residue |
| A | GLU311 |
| B | GLN502 |
| site_id | AF3 |
| Number of Residues | 22 |
| Details | binding site for residue PLS C 601 |
| Chain | Residue |
| C | SER82 |
| C | SER148 |
| C | GLY149 |
| C | SER150 |
| C | HIS177 |
| C | ALA231 |
| C | SER232 |
| C | ASP257 |
| C | ALA259 |
| C | HIS260 |
| C | THR283 |
| C | HIS285 |
| C | LYS286 |
| C | ARG430 |
| C | HOH816 |
| C | HOH1049 |
| D | TYR102 |
| D | GLU104 |
| D | TYR112 |
| D | GLY330 |
| D | GLY331 |
| D | HOH982 |
| site_id | AF4 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 602 |
| Chain | Residue |
| C | ILE167 |
| C | ALA169 |
| C | HIS180 |
| C | GLY181 |
| C | THR198 |
| C | MET199 |
| C | PRO200 |
| C | HOH714 |
| site_id | AF5 |
| Number of Residues | 9 |
| Details | binding site for residue MTX C 603 |
| Chain | Residue |
| C | TYR182 |
| C | THR184 |
| C | ASP185 |
| C | THR186 |
| C | LYS414 |
| C | ALA423 |
| D | GLU104 |
| D | TYR111 |
| D | HOH812 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 604 |
| Chain | Residue |
| C | TRP140 |
| C | PHE274 |
| C | ARG299 |
| C | HOH922 |
| C | HOH967 |
| C | HOH1030 |
| site_id | AF7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 605 |
| Chain | Residue |
| C | GLU61 |
| C | ASP64 |
| C | HOH745 |
| C | HOH999 |
| D | MET120 |
| site_id | AF8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 606 |
| Chain | Residue |
| C | LYS471 |
| C | LEU472 |
| C | LYS473 |
| C | HOH765 |
| C | HOH1043 |
| site_id | AF9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 607 |
| Chain | Residue |
| A | GLU368 |
| A | THR369 |
| C | VAL269 |
| C | ASP357 |
| C | HOH769 |
| C | HOH920 |
| site_id | AG1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 608 |
| Chain | Residue |
| C | ARG236 |
| C | HOH840 |
| C | HOH979 |
| site_id | AG2 |
| Number of Residues | 9 |
| Details | binding site for residue EDO C 609 |
| Chain | Residue |
| C | PRO151 |
| C | PHE154 |
| C | LEU328 |
| C | HOH717 |
| C | HOH867 |
| C | HOH930 |
| D | PRO151 |
| D | PHE154 |
| D | HOH842 |
| site_id | AG3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 610 |
| Chain | Residue |
| C | TYR375 |
| C | LYS394 |
| C | ASP454 |
| C | LYS458 |
| C | HOH710 |
| site_id | AG4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 611 |
| Chain | Residue |
| C | ASP445 |
| C | TYR499 |
| C | GLN502 |
| C | HOH739 |
| site_id | AG5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 612 |
| Chain | Residue |
| C | GLY95 |
| C | HOH782 |
| D | MET91 |
| D | GLY95 |
| D | HOH886 |
| site_id | AG6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 613 |
| Chain | Residue |
| C | THR505 |
| C | GLU509 |
| C | LYS510 |
| C | GLU511 |
| C | HOH770 |
| C | HOH848 |
| site_id | AG7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 614 |
| Chain | Residue |
| C | ALA159 |
| C | LEU160 |
| C | LYS162 |
| C | ARG319 |
| C | HOH863 |
| site_id | AG8 |
| Number of Residues | 1 |
| Details | binding site for residue EDO C 615 |
| Chain | Residue |
| C | ARG44 |
| site_id | AG9 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 616 |
| Chain | Residue |
| C | GLN322 |
| C | ALA323 |
| C | HOH911 |
| D | LYS187 |
| D | LYS188 |
| D | ILE189 |
| site_id | AH1 |
| Number of Residues | 8 |
| Details | binding site for residue MTX C 617 |
| Chain | Residue |
| A | ARG223 |
| C | TYR111 |
| D | THR184 |
| D | ASP185 |
| D | ILE189 |
| D | LYS414 |
| D | MET424 |
| D | HOH934 |
| site_id | AH2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 618 |
| Chain | Residue |
| C | LYS188 |
| C | ILE189 |
| D | GLN322 |
| D | HOH1031 |
| site_id | AH3 |
| Number of Residues | 9 |
| Details | binding site for residue EDO D 701 |
| Chain | Residue |
| D | ALA169 |
| D | ASP171 |
| D | HIS180 |
| D | GLY181 |
| D | THR198 |
| D | MET199 |
| D | PRO200 |
| D | HOH902 |
| D | HOH1049 |
| site_id | AH4 |
| Number of Residues | 8 |
| Details | binding site for residue SER D 702 |
| Chain | Residue |
| C | TYR102 |
| C | GLU104 |
| C | TYR112 |
| D | SER82 |
| D | SER232 |
| D | HIS260 |
| D | LLP286 |
| D | ARG430 |
| site_id | AH5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 703 |
| Chain | Residue |
| D | GLN126 |
| D | LEU130 |
| D | GLY141 |
| D | VAL142 |
| D | HOH918 |
| D | HOH939 |
| D | HOH1009 |
| site_id | AH6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 704 |
| Chain | Residue |
| D | TRP140 |
| D | PHE274 |
| D | HOH978 |
| site_id | AH7 |
| Number of Residues | 9 |
| Details | binding site for residue EDO D 705 |
| Chain | Residue |
| D | ASN206 |
| D | THR207 |
| D | GLY208 |
| D | VAL378 |
| D | SER379 |
| D | GLY380 |
| D | HOH888 |
| D | HOH892 |
| D | HOH973 |
| site_id | AH8 |
| Number of Residues | 7 |
| Details | binding site for residue EDO D 706 |
| Chain | Residue |
| C | ASP376 |
| C | ASN393 |
| D | ALA71 |
| D | LYS75 |
| D | TYR515 |
| D | GLU517 |
| D | HOH829 |
| site_id | AH9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 707 |
| Chain | Residue |
| D | TYR276 |
| D | ALA277 |
| D | ARG299 |
| D | TYR314 |
| D | HOH801 |
| site_id | AI1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 708 |
| Chain | Residue |
| D | ALA159 |
| D | LEU160 |
| D | LEU161 |
| D | LYS162 |
| D | ARG319 |
| D | HOH874 |
| site_id | AI2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 709 |
| Chain | Residue |
| D | ARG72 |
| D | GLU78 |
| D | GLU83 |
| D | ASN84 |
| D | PHE85 |
Functional Information from PROSITE/UniProt
| site_id | PS00096 |
| Number of Residues | 17 |
| Details | SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. DVvTTTTHKSLrGPRGA |
| Chain | Residue | Details |
| D | ASP278-ALA294 | |
| A | ASP278-ALA294 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 44 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"31873125","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SMN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6SMW","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"31873125","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SMN","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 4 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"31873125","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SMW","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
