2DFD
Crystal Structure of Human Malate Dehydrogenase Type 2
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003723 | molecular_function | RNA binding |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005759 | cellular_component | mitochondrial matrix |
| A | 0006094 | biological_process | gluconeogenesis |
| A | 0006099 | biological_process | tricarboxylic acid cycle |
| A | 0006107 | biological_process | oxaloacetate metabolic process |
| A | 0006108 | biological_process | malate metabolic process |
| A | 0006734 | biological_process | NADH metabolic process |
| A | 0009060 | biological_process | aerobic respiration |
| A | 0016020 | cellular_component | membrane |
| 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 | 0043490 | biological_process | malate-aspartate shuttle |
| A | 0043621 | molecular_function | obsolete protein self-association |
| A | 0046554 | molecular_function | L-malate dehydrogenase (NADP+) activity |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0003723 | molecular_function | RNA binding |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005759 | cellular_component | mitochondrial matrix |
| B | 0006094 | biological_process | gluconeogenesis |
| B | 0006099 | biological_process | tricarboxylic acid cycle |
| B | 0006107 | biological_process | oxaloacetate metabolic process |
| B | 0006108 | biological_process | malate metabolic process |
| B | 0006734 | biological_process | NADH metabolic process |
| B | 0009060 | biological_process | aerobic respiration |
| B | 0016020 | cellular_component | membrane |
| 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 | 0043490 | biological_process | malate-aspartate shuttle |
| B | 0043621 | molecular_function | obsolete protein self-association |
| B | 0046554 | molecular_function | L-malate dehydrogenase (NADP+) activity |
| B | 0070062 | cellular_component | extracellular exosome |
| C | 0003723 | molecular_function | RNA binding |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005759 | cellular_component | mitochondrial matrix |
| C | 0006094 | biological_process | gluconeogenesis |
| C | 0006099 | biological_process | tricarboxylic acid cycle |
| C | 0006107 | biological_process | oxaloacetate metabolic process |
| C | 0006108 | biological_process | malate metabolic process |
| C | 0006734 | biological_process | NADH metabolic process |
| C | 0009060 | biological_process | aerobic respiration |
| C | 0016020 | cellular_component | membrane |
| 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 | 0043490 | biological_process | malate-aspartate shuttle |
| C | 0043621 | molecular_function | obsolete protein self-association |
| C | 0046554 | molecular_function | L-malate dehydrogenase (NADP+) activity |
| C | 0070062 | cellular_component | extracellular exosome |
| D | 0003723 | molecular_function | RNA binding |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0005634 | cellular_component | nucleus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005759 | cellular_component | mitochondrial matrix |
| D | 0006094 | biological_process | gluconeogenesis |
| D | 0006099 | biological_process | tricarboxylic acid cycle |
| D | 0006107 | biological_process | oxaloacetate metabolic process |
| D | 0006108 | biological_process | malate metabolic process |
| D | 0006734 | biological_process | NADH metabolic process |
| D | 0009060 | biological_process | aerobic respiration |
| D | 0016020 | cellular_component | membrane |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016615 | molecular_function | malate dehydrogenase activity |
| D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| D | 0019752 | biological_process | carboxylic acid metabolic process |
| D | 0030060 | molecular_function | L-malate dehydrogenase (NAD+) activity |
| D | 0043490 | biological_process | malate-aspartate shuttle |
| D | 0043621 | molecular_function | obsolete protein self-association |
| D | 0046554 | molecular_function | L-malate dehydrogenase (NADP+) activity |
| D | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MLT D 3101 |
| Chain | Residue |
| D | ARG86 |
| D | ARG92 |
| D | ASN124 |
| D | ARG158 |
| D | HIS182 |
| D | GLY216 |
| D | NAD3004 |
| D | HOH3399 |
| D | HOH3400 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MLT B 3102 |
| Chain | Residue |
| B | ARG86 |
| B | ARG92 |
| B | ASN124 |
| B | ARG158 |
| B | HIS182 |
| B | GLY216 |
| B | NAD3001 |
| B | HOH3405 |
| B | HOH3528 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE MLT C 3103 |
| Chain | Residue |
| C | ARG86 |
| C | ARG92 |
| C | ASN124 |
| C | ARG158 |
| C | HIS182 |
| C | GLY216 |
| C | ALA229 |
| C | NAD3002 |
| C | HOH3509 |
| C | HOH3729 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE MLT A 3104 |
| Chain | Residue |
| A | ARG86 |
| A | ARG92 |
| A | ASN124 |
| A | ARG158 |
| A | HIS182 |
| A | GLY216 |
| A | ALA229 |
| A | NAD3003 |
| A | HOH3337 |
| A | HOH3341 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL C 3201 |
| Chain | Residue |
| C | ARG92 |
| C | HOH3553 |
| site_id | AC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL D 3202 |
| Chain | Residue |
| D | ARG92 |
| D | HOH3318 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CL A 3203 |
| Chain | Residue |
| A | ARG92 |
| site_id | AC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL C 3204 |
| Chain | Residue |
| C | GLN263 |
| C | HOH3597 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE CL A 3205 |
| Chain | Residue |
| A | ASN146 |
| site_id | BC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE CL B 3206 |
| Chain | Residue |
| B | VAL198 |
| B | PHE200 |
| B | HOH3533 |
| site_id | BC2 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE CL D 3207 |
| Chain | Residue |
| D | VAL198 |
| D | HOH3416 |
| site_id | BC3 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE NAD B 3001 |
| Chain | Residue |
| B | SER15 |
| B | GLY16 |
| B | GLY17 |
| B | ILE18 |
| B | TYR38 |
| B | ASP39 |
| B | ILE40 |
| B | PRO81 |
| B | ALA82 |
| B | GLY83 |
| B | VAL84 |
| B | PRO85 |
| B | ASN99 |
| B | ILE102 |
| B | ILE122 |
| B | ASN124 |
| B | VAL151 |
| B | HIS182 |
| B | ALA229 |
| B | THR230 |
| B | MET233 |
| B | MLT3102 |
| B | HOH3404 |
| B | HOH3405 |
| B | HOH3415 |
| B | HOH3420 |
| B | HOH3429 |
| B | HOH3452 |
| B | HOH3476 |
| B | HOH3497 |
| B | HOH3501 |
| B | HOH3519 |
| B | HOH3527 |
| site_id | BC4 |
| Number of Residues | 35 |
| Details | BINDING SITE FOR RESIDUE NAD C 3002 |
| Chain | Residue |
| C | ILE102 |
| C | ILE122 |
| C | ASN124 |
| C | VAL126 |
| C | VAL151 |
| C | HIS182 |
| C | ALA229 |
| C | THR230 |
| C | MET233 |
| C | MLT3103 |
| C | HOH3509 |
| C | HOH3520 |
| C | HOH3526 |
| C | HOH3540 |
| C | HOH3557 |
| C | HOH3626 |
| C | HOH3636 |
| C | HOH3646 |
| C | HOH3691 |
| C | HOH3730 |
| C | GLY13 |
| C | SER15 |
| C | GLY16 |
| C | GLY17 |
| C | ILE18 |
| C | TYR38 |
| C | ASP39 |
| C | ILE40 |
| C | PRO81 |
| C | ALA82 |
| C | GLY83 |
| C | VAL84 |
| C | PRO85 |
| C | LEU95 |
| C | ASN99 |
| site_id | BC5 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE NAD A 3003 |
| Chain | Residue |
| A | SER15 |
| A | GLY16 |
| A | GLY17 |
| A | ILE18 |
| A | TYR38 |
| A | ASP39 |
| A | ILE40 |
| A | PRO81 |
| A | ALA82 |
| A | GLY83 |
| A | VAL84 |
| A | PRO85 |
| A | ASN99 |
| A | ILE102 |
| A | ILE122 |
| A | ASN124 |
| A | VAL126 |
| A | VAL151 |
| A | HIS182 |
| A | ALA229 |
| A | THR230 |
| A | MET233 |
| A | MLT3104 |
| A | HOH3304 |
| A | HOH3305 |
| A | HOH3337 |
| A | HOH3344 |
| A | HOH3347 |
| A | HOH3379 |
| A | HOH3389 |
| A | HOH3427 |
| A | HOH3476 |
| A | HOH3478 |
| site_id | BC6 |
| Number of Residues | 35 |
| Details | BINDING SITE FOR RESIDUE NAD D 3004 |
| Chain | Residue |
| D | SER15 |
| D | GLY16 |
| D | GLY17 |
| D | ILE18 |
| D | TYR38 |
| D | ASP39 |
| D | ILE40 |
| D | PRO81 |
| D | ALA82 |
| D | GLY83 |
| D | VAL84 |
| D | PRO85 |
| D | LEU95 |
| D | ASN99 |
| D | ILE102 |
| D | ILE122 |
| D | ASN124 |
| D | VAL126 |
| D | VAL151 |
| D | HIS182 |
| D | ALA229 |
| D | THR230 |
| D | MET233 |
| D | MLT3101 |
| D | HOH3220 |
| D | HOH3224 |
| D | HOH3236 |
| D | HOH3237 |
| D | HOH3251 |
| D | HOH3313 |
| D | HOH3335 |
| D | HOH3341 |
| D | HOH3361 |
| D | HOH3393 |
| D | HOH3399 |
| site_id | BC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE HIS A 3301 |
| Chain | Residue |
| A | ASN160 |
| A | PRO171 |
| A | ALA172 |
| A | VAL174 |
| A | ASN175 |
| A | ARG239 |
| A | ALA3302 |
| B | GLU54 |
| B | HOH3434 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ALA A 3302 |
| Chain | Residue |
| A | ARG239 |
| A | SER243 |
| A | HIS3301 |
| A | HOH3359 |
| site_id | BC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE HIS B 3401 |
| Chain | Residue |
| A | GLU54 |
| B | ASN160 |
| B | PRO171 |
| B | ALA172 |
| B | VAL174 |
| B | ASN175 |
| B | ARG239 |
| site_id | CC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE HIS C 3501 |
| Chain | Residue |
| C | ASN160 |
| C | PRO171 |
| C | ALA172 |
| C | VAL174 |
| C | ASN175 |
| C | ARG239 |
| D | GLU54 |
Functional Information from PROSITE/UniProt
| site_id | PS00068 |
| Number of Residues | 13 |
| Details | MDH Malate dehydrogenase active site signature. VTTLDivRAntfV |
| Chain | Residue | Details |
| A | VAL151-VAL163 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P00346 |
| Chain | Residue | Details |
| A | GLY184 | |
| B | GLY184 | |
| C | GLY184 | |
| D | GLY184 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | BINDING: BINDING => ECO:0000269|Ref.16 |
| Chain | Residue | Details |
| A | SER15 | |
| B | TYR235 | |
| C | SER15 | |
| C | ALA41 | |
| C | THR101 | |
| C | ASN124 | |
| C | TYR235 | |
| D | SER15 | |
| D | ALA41 | |
| D | THR101 | |
| D | ASN124 | |
| A | ALA41 | |
| D | TYR235 | |
| A | THR101 | |
| A | ASN124 | |
| A | TYR235 | |
| B | SER15 | |
| B | ALA41 | |
| B | THR101 | |
| B | ASN124 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU10004, ECO:0000269|Ref.16 |
| Chain | Residue | Details |
| A | PRO88 | |
| C | ASP94 | |
| C | VAL126 | |
| C | ASN160 | |
| D | PRO88 | |
| D | ASP94 | |
| D | VAL126 | |
| D | ASN160 | |
| A | ASP94 | |
| A | VAL126 | |
| A | ASN160 | |
| B | PRO88 | |
| B | ASP94 | |
| B | VAL126 | |
| B | ASN160 | |
| C | PRO88 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 36 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P08249 |
| Chain | Residue | Details |
| A | TYR62 | |
| B | TYR62 | |
| B | CYS75 | |
| B | LEU169 | |
| B | ASP199 | |
| B | GLY280 | |
| B | SER291 | |
| B | ILE298 | |
| B | SER308 | |
| B | LEU319 | |
| C | TYR62 | |
| A | CYS75 | |
| C | CYS75 | |
| C | LEU169 | |
| C | ASP199 | |
| C | GLY280 | |
| C | SER291 | |
| C | ILE298 | |
| C | SER308 | |
| C | LEU319 | |
| D | TYR62 | |
| D | CYS75 | |
| A | LEU169 | |
| D | LEU169 | |
| D | ASP199 | |
| D | GLY280 | |
| D | SER291 | |
| D | ILE298 | |
| D | SER308 | |
| D | LEU319 | |
| A | ASP199 | |
| A | GLY280 | |
| A | SER291 | |
| A | ILE298 | |
| A | SER308 | |
| A | LEU319 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | PHE149 | |
| B | PHE149 | |
| C | PHE149 | |
| D | PHE149 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P08249 |
| Chain | Residue | Details |
| A | ILE187 | |
| A | GLY253 | |
| B | ILE187 | |
| B | GLY253 | |
| C | ILE187 | |
| C | GLY253 | |
| D | ILE187 | |
| D | GLY253 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q32LG3 |
| Chain | Residue | Details |
| A | LYS223 | |
| D | LYS223 | |
| D | LEU285 | |
| D | GLY312 | |
| A | LEU285 | |
| A | GLY312 | |
| B | LYS223 | |
| B | LEU285 | |
| B | GLY312 | |
| C | LYS223 | |
| C | LEU285 | |
| C | GLY312 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | THR230 | |
| A | LYS310 | |
| B | THR230 | |
| B | LYS310 | |
| C | THR230 | |
| C | LYS310 | |
| D | THR230 | |
| D | LYS310 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-malonyllysine; alternate => ECO:0000250|UniProtKB:Q32LG3 |
| Chain | Residue | Details |
| A | GLU313 | |
| B | GLU313 | |
| C | GLU313 | |
| D | GLU313 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P04636 |
| Chain | Residue | Details |
| A | GLY17 | |
| B | GLY17 | |
| C | GLY17 | |
| D | GLY17 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| A | ASP155 | |
| A | HIS182 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| B | ASP155 | |
| B | HIS182 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| C | ASP155 | |
| C | HIS182 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| D | ASP155 | |
| D | HIS182 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| A | ASP155 | |
| A | HIS182 | |
| A | ARG158 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| B | ASP155 | |
| B | HIS182 | |
| B | ARG158 |
| site_id | CSA7 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| C | ASP155 | |
| C | HIS182 | |
| C | ARG158 |
| site_id | CSA8 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1emd |
| Chain | Residue | Details |
| D | ASP155 | |
| D | HIS182 | |
| D | ARG158 |
