5NUE
Cytosolic Malate Dehydrogenase 1 (peroxide-treated)
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000325 | cellular_component | plant-type vacuole |
| A | 0003729 | molecular_function | mRNA binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005794 | cellular_component | Golgi apparatus |
| A | 0005829 | cellular_component | cytosol |
| A | 0005886 | cellular_component | plasma membrane |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0006108 | biological_process | malate metabolic process |
| A | 0009506 | cellular_component | plasmodesma |
| A | 0009507 | cellular_component | chloroplast |
| A | 0009570 | cellular_component | chloroplast stroma |
| A | 0010043 | biological_process | response to zinc ion |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016615 | molecular_function | malate dehydrogenase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| A | 0048046 | cellular_component | apoplast |
| B | 0000325 | cellular_component | plant-type vacuole |
| B | 0003729 | molecular_function | mRNA binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005794 | cellular_component | Golgi apparatus |
| B | 0005829 | cellular_component | cytosol |
| B | 0005886 | cellular_component | plasma membrane |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0006108 | biological_process | malate metabolic process |
| B | 0009506 | cellular_component | plasmodesma |
| B | 0009507 | cellular_component | chloroplast |
| B | 0009570 | cellular_component | chloroplast stroma |
| B | 0010043 | biological_process | response to zinc ion |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016615 | molecular_function | malate dehydrogenase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| B | 0048046 | cellular_component | apoplast |
| C | 0000325 | cellular_component | plant-type vacuole |
| C | 0003729 | molecular_function | mRNA binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005576 | cellular_component | extracellular region |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005794 | cellular_component | Golgi apparatus |
| C | 0005829 | cellular_component | cytosol |
| C | 0005886 | cellular_component | plasma membrane |
| C | 0006099 | biological_process | tricarboxylic acid cycle |
| C | 0006108 | biological_process | malate metabolic process |
| C | 0009506 | cellular_component | plasmodesma |
| C | 0009507 | cellular_component | chloroplast |
| C | 0009570 | cellular_component | chloroplast stroma |
| C | 0010043 | biological_process | response to zinc ion |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016615 | molecular_function | malate dehydrogenase activity |
| C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| C | 0019752 | biological_process | carboxylic acid metabolic process |
| C | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| C | 0048046 | cellular_component | apoplast |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 33 |
| Details | binding site for residue NAD A 401 |
| Chain | Residue |
| A | GLY12 |
| A | PHE91 |
| A | PRO92 |
| A | ILE109 |
| A | GLN113 |
| A | VAL130 |
| A | ALA131 |
| A | ASN132 |
| A | LEU156 |
| A | HIS188 |
| A | SER243 |
| A | GLY15 |
| A | SO4402 |
| A | HOH517 |
| A | HOH553 |
| A | HOH561 |
| A | HOH564 |
| A | HOH567 |
| A | HOH570 |
| A | HOH571 |
| A | HOH589 |
| A | HOH599 |
| A | GLN16 |
| A | HOH600 |
| A | HOH614 |
| A | HOH631 |
| A | HOH655 |
| A | ILE17 |
| A | ASP43 |
| A | ILE44 |
| A | VAL88 |
| A | GLY89 |
| A | GLY90 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 A 402 |
| Chain | Residue |
| A | ASN132 |
| A | ARG163 |
| A | HIS188 |
| A | GLY232 |
| A | SER243 |
| A | NAD401 |
| A | HOH565 |
| A | HOH611 |
| A | HOH674 |
| A | HOH679 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 A 403 |
| Chain | Residue |
| A | ARG7 |
| A | ILE38 |
| A | HIS40 |
| A | VAL70 |
| A | HOH508 |
| A | HOH520 |
| site_id | AC4 |
| Number of Residues | 9 |
| Details | binding site for residue GOL A 404 |
| Chain | Residue |
| A | ILE299 |
| A | VAL300 |
| A | GLN301 |
| A | HOH537 |
| B | LYS100 |
| B | ASP101 |
| B | MET103 |
| B | SER104 |
| B | LEU326 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue GOL A 405 |
| Chain | Residue |
| A | GLN202 |
| A | GLY206 |
| A | GLU207 |
| A | HOH514 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue PEO A 406 |
| Chain | Residue |
| A | ARG163 |
| A | GLY166 |
| A | GLN167 |
| A | ARG231 |
| B | ILE59 |
| B | ASP60 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue PEO A 407 |
| Chain | Residue |
| A | ASP253 |
| A | HOH598 |
| A | HOH640 |
| B | ARG27 |
| B | ALA61 |
| B | ALA62 |
| B | HOH628 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue PEO A 408 |
| Chain | Residue |
| A | LYS142 |
| A | GLU143 |
| A | PRO146 |
| A | HOH507 |
| A | HOH601 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 409 |
| Chain | Residue |
| A | SER190 |
| A | GLN230 |
| A | HOH531 |
| A | HOH597 |
| site_id | AD1 |
| Number of Residues | 4 |
| Details | binding site for residue TRS A 410 |
| Chain | Residue |
| A | LYS215 |
| A | ASP216 |
| A | ASP217 |
| A | ALA218 |
| site_id | AD2 |
| Number of Residues | 7 |
| Details | binding site for residue ETX A 411 |
| Chain | Residue |
| A | GLN167 |
| A | ARG231 |
| A | HOH709 |
| A | HOH760 |
| B | SME56 |
| B | ILE59 |
| C | HOH792 |
| site_id | AD3 |
| Number of Residues | 34 |
| Details | binding site for residue NAD B 401 |
| Chain | Residue |
| B | ILE17 |
| B | ASP43 |
| B | ILE44 |
| B | VAL88 |
| B | GLY89 |
| B | GLY90 |
| B | PHE91 |
| B | PRO92 |
| B | ILE109 |
| B | GLN113 |
| B | VAL130 |
| B | ALA131 |
| B | ASN132 |
| B | LEU156 |
| B | HIS188 |
| B | SER242 |
| B | SER243 |
| B | SO4404 |
| B | PEO411 |
| B | HOH503 |
| B | HOH512 |
| B | HOH561 |
| B | HOH562 |
| B | HOH564 |
| B | HOH585 |
| B | HOH599 |
| B | HOH604 |
| B | HOH648 |
| B | HOH670 |
| B | HOH682 |
| B | GLY12 |
| B | ALA14 |
| B | GLY15 |
| B | GLN16 |
| site_id | AD4 |
| Number of Residues | 8 |
| Details | binding site for residue SO4 B 402 |
| Chain | Residue |
| B | GLU98 |
| B | ARG99 |
| B | SER189 |
| B | SER190 |
| B | HOH592 |
| B | HOH632 |
| B | HOH654 |
| B | HOH683 |
| site_id | AD5 |
| Number of Residues | 9 |
| Details | binding site for residue SO4 B 403 |
| Chain | Residue |
| B | ARG7 |
| B | ILE38 |
| B | HIS40 |
| B | VAL70 |
| B | HOH502 |
| B | HOH504 |
| B | HOH571 |
| B | HOH621 |
| C | GLU170 |
| site_id | AD6 |
| Number of Residues | 11 |
| Details | binding site for residue SO4 B 404 |
| Chain | Residue |
| B | ARG93 |
| B | ARG99 |
| B | ASN132 |
| B | ARG163 |
| B | HIS188 |
| B | GLY232 |
| B | SER243 |
| B | NAD401 |
| B | PEO411 |
| B | EDO417 |
| B | HOH549 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 405 |
| Chain | Residue |
| A | ILE59 |
| B | GLN167 |
| B | ARG231 |
| B | HOH555 |
| B | HOH581 |
| B | HOH607 |
| site_id | AD8 |
| Number of Residues | 5 |
| Details | binding site for residue GOL B 406 |
| Chain | Residue |
| B | ASN83 |
| B | ASN124 |
| B | LYS126 |
| B | HOH541 |
| B | HOH749 |
| site_id | AD9 |
| Number of Residues | 8 |
| Details | binding site for residue GOL B 407 |
| Chain | Residue |
| A | ARG239 |
| A | HOH683 |
| B | ALA14 |
| B | GLY15 |
| B | GLN16 |
| B | HOH511 |
| B | HOH547 |
| B | HOH630 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue PEO B 408 |
| Chain | Residue |
| A | ASP60 |
| B | ARG163 |
| B | GLN167 |
| B | ARG231 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue PEO B 409 |
| Chain | Residue |
| B | LYS142 |
| B | GLU143 |
| B | PRO146 |
| B | HOH536 |
| site_id | AE3 |
| Number of Residues | 8 |
| Details | binding site for residue PEO B 410 |
| Chain | Residue |
| A | VAL176 |
| A | HOH555 |
| B | ILE59 |
| B | PHE63 |
| B | LEU66 |
| B | HOH507 |
| B | HOH530 |
| B | HOH583 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue PEO B 411 |
| Chain | Residue |
| B | GLY232 |
| B | SER242 |
| B | SER243 |
| B | NAD401 |
| B | SO4404 |
| site_id | AE5 |
| Number of Residues | 5 |
| Details | binding site for residue ACT B 412 |
| Chain | Residue |
| B | ASP216 |
| B | ASP217 |
| B | ALA218 |
| C | GLU318 |
| C | LYS321 |
| site_id | AE6 |
| Number of Residues | 2 |
| Details | binding site for residue ACT B 413 |
| Chain | Residue |
| B | PRO149 |
| B | GLU150 |
| site_id | AE7 |
| Number of Residues | 4 |
| Details | binding site for residue ACT B 414 |
| Chain | Residue |
| B | PRO281 |
| B | SER282 |
| B | HOH509 |
| B | HOH663 |
| site_id | AE8 |
| Number of Residues | 2 |
| Details | binding site for residue FMT B 415 |
| Chain | Residue |
| B | GLY206 |
| B | GLU207 |
| site_id | AE9 |
| Number of Residues | 2 |
| Details | binding site for residue FMT B 416 |
| Chain | Residue |
| B | LYS111 |
| B | SER332 |
| site_id | AF1 |
| Number of Residues | 10 |
| Details | binding site for residue EDO B 417 |
| Chain | Residue |
| B | ARG99 |
| B | ASP160 |
| B | ARG163 |
| B | GLN192 |
| B | VAL228 |
| B | GLN229 |
| B | ARG231 |
| B | GLY232 |
| B | SO4404 |
| B | HOH613 |
| site_id | AF2 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 418 |
| Chain | Residue |
| A | LYS180 |
| A | LYS200 |
| A | GLU207 |
| B | ASP325 |
| B | TYR328 |
| B | SER329 |
| B | HOH685 |
| B | HOH734 |
| site_id | AF3 |
| Number of Residues | 33 |
| Details | binding site for residue NAD C 401 |
| Chain | Residue |
| C | GLY12 |
| C | GLY15 |
| C | GLN16 |
| C | ILE17 |
| C | ASP43 |
| C | ILE44 |
| C | VAL88 |
| C | GLY89 |
| C | GLY90 |
| C | PHE91 |
| C | PRO92 |
| C | ILE109 |
| C | GLN113 |
| C | VAL130 |
| C | ALA131 |
| C | ASN132 |
| C | LEU156 |
| C | HIS188 |
| C | SER243 |
| C | SO4402 |
| C | PEO407 |
| C | HOH520 |
| C | HOH547 |
| C | HOH554 |
| C | HOH585 |
| C | HOH593 |
| C | HOH598 |
| C | HOH601 |
| C | HOH603 |
| C | HOH604 |
| C | HOH625 |
| C | HOH658 |
| C | HOH695 |
| site_id | AF4 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 C 402 |
| Chain | Residue |
| C | ASN132 |
| C | ARG163 |
| C | HIS188 |
| C | GLY232 |
| C | SER243 |
| C | NAD401 |
| C | HOH578 |
| C | HOH620 |
| C | HOH693 |
| C | HOH741 |
| site_id | AF5 |
| Number of Residues | 10 |
| Details | binding site for residue SO4 C 403 |
| Chain | Residue |
| A | GLU170 |
| A | HOH652 |
| B | HOH780 |
| C | ARG7 |
| C | ILE38 |
| C | HIS40 |
| C | VAL70 |
| C | HOH501 |
| C | HOH599 |
| C | HOH629 |
| site_id | AF6 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 C 404 |
| Chain | Residue |
| A | ARG171 |
| A | GLU223 |
| A | HOH781 |
| C | ALA122 |
| C | PRO123 |
| C | ASN124 |
| C | HOH674 |
| site_id | AF7 |
| Number of Residues | 7 |
| Details | binding site for residue GOL C 405 |
| Chain | Residue |
| C | SER277 |
| C | TYR278 |
| C | GLN301 |
| C | GLY302 |
| C | EDO412 |
| C | HOH642 |
| C | HOH725 |
| site_id | AF8 |
| Number of Residues | 6 |
| Details | binding site for residue PEO C 406 |
| Chain | Residue |
| C | ILE59 |
| C | ASP60 |
| C | ARG163 |
| C | GLY166 |
| C | GLN167 |
| C | ARG231 |
| site_id | AF9 |
| Number of Residues | 5 |
| Details | binding site for residue PEO C 407 |
| Chain | Residue |
| C | ILE44 |
| C | NAD401 |
| C | HOH549 |
| C | HOH552 |
| C | HOH631 |
| site_id | AG1 |
| Number of Residues | 7 |
| Details | binding site for residue PEO C 408 |
| Chain | Residue |
| C | ILE59 |
| C | PHE63 |
| C | LEU66 |
| C | VAL176 |
| C | HOH504 |
| C | HOH590 |
| C | HOH699 |
| site_id | AG2 |
| Number of Residues | 7 |
| Details | binding site for residue PEO C 409 |
| Chain | Residue |
| C | GLN16 |
| C | TYR19 |
| C | ARG239 |
| C | HOH521 |
| C | HOH521 |
| C | HOH662 |
| C | HOH712 |
| site_id | AG3 |
| Number of Residues | 4 |
| Details | binding site for residue FMT C 410 |
| Chain | Residue |
| C | SER190 |
| C | GLN230 |
| C | HOH519 |
| C | HOH656 |
| site_id | AG4 |
| Number of Residues | 7 |
| Details | binding site for residue FMT C 411 |
| Chain | Residue |
| C | VAL259 |
| C | LEU260 |
| C | GLY261 |
| C | ARG293 |
| C | ASN294 |
| C | HOH508 |
| C | HOH678 |
| site_id | AG5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO C 412 |
| Chain | Residue |
| C | TYR278 |
| C | SER279 |
| C | ARG310 |
| C | GOL405 |
| C | HOH507 |
| C | HOH723 |
Functional Information from PROSITE/UniProt
| site_id | PS00068 |
| Number of Residues | 13 |
| Details | MDH Malate dehydrogenase active site signature. LTRLDhnRAlgqI |
| Chain | Residue | Details |
| B | LEU156-ILE168 | |
| C | LEU156-ILE168 | |
| A | LEU156-ILE168 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 1 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P11708 |
| Chain | Residue | Details |
| C | HIS188 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 9 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:29194485, ECO:0007744|PDB:5NUE, ECO:0007744|PDB:5NUF |
| Chain | Residue | Details |
| C | GLN16 | |
| C | ASP43 | |
| C | GLY90 | |
| C | ARG99 | |
| C | GLN113 | |
| C | ASN132 | |
| C | ARG163 | |
| C | HIS188 | |
| C | SER243 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | MOD_RES: Methionine sulfoxide => ECO:0000269|PubMed:29194485 |
| Chain | Residue | Details |
| C | SME56 | |
| C | MET97 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:19292762 |
| Chain | Residue | Details |
| C | LYS119 |
