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 | 0005747 | cellular_component | obsolete mitochondrial respiratory chain complex I |
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 | 0009536 | cellular_component | plastid |
A | 0016740 | molecular_function | transferase activity |
A | 0019264 | biological_process | glycine biosynthetic process from serine |
A | 0030170 | molecular_function | pyridoxal phosphate binding |
A | 0035999 | biological_process | tetrahydrofolate interconversion |
A | 0050897 | molecular_function | cobalt ion binding |
B | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
B | 0005739 | cellular_component | mitochondrion |
B | 0005747 | cellular_component | obsolete mitochondrial respiratory chain complex I |
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 | 0009536 | cellular_component | plastid |
B | 0016740 | molecular_function | transferase activity |
B | 0019264 | biological_process | glycine biosynthetic process from serine |
B | 0030170 | molecular_function | pyridoxal phosphate binding |
B | 0035999 | biological_process | tetrahydrofolate interconversion |
B | 0050897 | molecular_function | cobalt ion binding |
C | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
C | 0005739 | cellular_component | mitochondrion |
C | 0005747 | cellular_component | obsolete mitochondrial respiratory chain complex I |
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 | 0009536 | cellular_component | plastid |
C | 0016740 | molecular_function | transferase activity |
C | 0019264 | biological_process | glycine biosynthetic process from serine |
C | 0030170 | molecular_function | pyridoxal phosphate binding |
C | 0035999 | biological_process | tetrahydrofolate interconversion |
C | 0050897 | molecular_function | cobalt ion binding |
D | 0004372 | molecular_function | glycine hydroxymethyltransferase activity |
D | 0005739 | cellular_component | mitochondrion |
D | 0005747 | cellular_component | obsolete mitochondrial respiratory chain complex I |
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 | 0009536 | cellular_component | plastid |
D | 0016740 | molecular_function | transferase activity |
D | 0019264 | biological_process | glycine biosynthetic process from serine |
D | 0030170 | molecular_function | pyridoxal phosphate binding |
D | 0035999 | biological_process | tetrahydrofolate interconversion |
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 |
A | ASP278-ALA294 | |
D | ASP278-ALA294 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 10 |
Details | BINDING: BINDING => ECO:0000269|PubMed:31873125, ECO:0007744|PDB:6SMN, ECO:0007744|PDB:6SMW |
Chain | Residue | Details |
D | SER82 | |
D | ARG430 | |
B | SER82 | |
B | TYR102 | |
B | GLU104 | |
B | TYR112 | |
B | SER148 | |
B | SER232 | |
B | HIS260 | |
B | GLY331 | |
B | LYS414 | |
D | TYR102 | |
B | ARG430 | |
C | SER82 | |
C | TYR102 | |
C | GLU104 | |
C | TYR112 | |
C | SER148 | |
C | SER232 | |
C | HIS260 | |
C | GLY331 | |
C | LYS414 | |
D | GLU104 | |
C | ARG430 | |
D | TYR112 | |
D | SER148 | |
D | SER232 | |
D | HIS260 | |
D | GLY331 | |
D | LYS414 |
site_id | SWS_FT_FI2 |
Number of Residues | 2 |
Details | BINDING: BINDING => ECO:0000269|PubMed:31873125, ECO:0007744|PDB:6SMN |
Chain | Residue | Details |
D | HIS177 | |
D | THR184 | |
B | HIS177 | |
B | THR184 | |
C | HIS177 | |
C | THR184 |
site_id | SWS_FT_FI3 |
Number of Residues | 1 |
Details | BINDING: BINDING => ECO:0000269|PubMed:31873125, ECO:0007744|PDB:6SMW |
Chain | Residue | Details |
D | LLP286 | |
B | LYS286 | |
C | LYS286 |
site_id | SWS_FT_FI4 |
Number of Residues | 1 |
Details | MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000250 |
Chain | Residue | Details |
D | LLP286 | |
B | LYS286 | |
C | LYS286 |