4WLV
Crystal structure of NAD bound MDH2
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 | 27 |
| Details | binding site for residue NAD A 401 |
| Chain | Residue |
| A | SER33 |
| A | GLY101 |
| A | VAL102 |
| A | PRO103 |
| A | LEU113 |
| A | ASN117 |
| A | ILE120 |
| A | ILE140 |
| A | ALA141 |
| A | ASN142 |
| A | VAL169 |
| A | GLY34 |
| A | HIS200 |
| A | ALA247 |
| A | MET251 |
| A | PO4402 |
| A | PO4403 |
| A | HOH510 |
| A | HOH515 |
| A | HOH520 |
| A | GLY35 |
| A | ILE36 |
| A | TYR56 |
| A | ASP57 |
| A | ILE58 |
| A | PRO99 |
| A | ALA100 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue PO4 A 402 |
| Chain | Residue |
| A | PRO103 |
| A | ARG104 |
| A | ARG110 |
| A | ASN142 |
| A | SER246 |
| A | NAD401 |
| A | PO4403 |
| site_id | AC3 |
| Number of Residues | 8 |
| Details | binding site for residue PO4 A 403 |
| Chain | Residue |
| A | ARG104 |
| A | ARG110 |
| A | ASN142 |
| A | ARG176 |
| A | HIS200 |
| A | GLY234 |
| A | NAD401 |
| A | PO4402 |
| site_id | AC4 |
| Number of Residues | 24 |
| Details | binding site for residue NAD B 401 |
| Chain | Residue |
| B | SER33 |
| B | GLY34 |
| B | GLY35 |
| B | ILE36 |
| B | TYR56 |
| B | ASP57 |
| B | ILE58 |
| B | PRO99 |
| B | ALA100 |
| B | GLY101 |
| B | VAL102 |
| B | PRO103 |
| B | ASN117 |
| B | ILE120 |
| B | ILE140 |
| B | ASN142 |
| B | VAL169 |
| B | HIS200 |
| B | ALA247 |
| B | THR248 |
| B | MET251 |
| B | PO4402 |
| B | PO4403 |
| B | HOH511 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | binding site for residue PO4 B 402 |
| Chain | Residue |
| B | PRO103 |
| B | ARG104 |
| B | LEU113 |
| B | ASN142 |
| B | SER246 |
| B | NAD401 |
| B | PO4403 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue PO4 B 403 |
| Chain | Residue |
| B | ARG104 |
| B | ARG110 |
| B | ASN142 |
| B | ARG176 |
| B | HIS200 |
| B | GLY234 |
| B | NAD401 |
| B | PO4402 |
| site_id | AC7 |
| Number of Residues | 25 |
| Details | binding site for residue NAD C 401 |
| Chain | Residue |
| C | THR248 |
| C | MET251 |
| C | PO4402 |
| C | PO4403 |
| C | HOH505 |
| C | HOH507 |
| C | HOH508 |
| C | SER33 |
| C | GLY34 |
| C | GLY35 |
| C | ILE36 |
| C | TYR56 |
| C | ASP57 |
| C | ILE58 |
| C | PRO99 |
| C | ALA100 |
| C | GLY101 |
| C | VAL102 |
| C | PRO103 |
| C | ASN117 |
| C | ILE140 |
| C | ASN142 |
| C | VAL169 |
| C | HIS200 |
| C | ALA247 |
| site_id | AC8 |
| Number of Residues | 7 |
| Details | binding site for residue PO4 C 402 |
| Chain | Residue |
| C | PRO103 |
| C | ARG104 |
| C | LEU113 |
| C | ASN142 |
| C | SER246 |
| C | NAD401 |
| C | PO4403 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue PO4 C 403 |
| Chain | Residue |
| C | ARG104 |
| C | ARG110 |
| C | ASN142 |
| C | ARG176 |
| C | HIS200 |
| C | GLY234 |
| C | NAD401 |
| C | PO4402 |
| site_id | AD1 |
| Number of Residues | 24 |
| Details | binding site for residue NAD D 401 |
| Chain | Residue |
| D | SER33 |
| D | GLY34 |
| D | GLY35 |
| D | ILE36 |
| D | TYR56 |
| D | ASP57 |
| D | ILE58 |
| D | PRO99 |
| D | ALA100 |
| D | GLY101 |
| D | VAL102 |
| D | PRO103 |
| D | ASN117 |
| D | ILE120 |
| D | ILE140 |
| D | ASN142 |
| D | VAL169 |
| D | HIS200 |
| D | ALA247 |
| D | THR248 |
| D | MET251 |
| D | PO4402 |
| D | PO4403 |
| D | HOH504 |
| site_id | AD2 |
| Number of Residues | 8 |
| Details | binding site for residue PO4 D 402 |
| Chain | Residue |
| D | ARG104 |
| D | ARG110 |
| D | ASN142 |
| D | ARG176 |
| D | HIS200 |
| D | GLY234 |
| D | NAD401 |
| D | PO4403 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue PO4 D 403 |
| Chain | Residue |
| D | PRO103 |
| D | ARG104 |
| D | ASN142 |
| D | SER246 |
| D | NAD401 |
| D | PO4402 |
Functional Information from PROSITE/UniProt
| site_id | PS00068 |
| Number of Residues | 13 |
| Details | MDH Malate dehydrogenase active site signature. VTTLDivRAntfV |
| Chain | Residue | Details |
| A | VAL169-VAL181 |
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 | HIS200 | |
| B | HIS200 | |
| C | HIS200 | |
| D | HIS200 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 20 |
| Details | BINDING: BINDING => ECO:0000269|Ref.16 |
| Chain | Residue | Details |
| A | GLY31 | |
| B | MET251 | |
| C | GLY31 | |
| C | ASP57 | |
| C | ASN117 | |
| C | ILE140 | |
| C | MET251 | |
| D | GLY31 | |
| D | ASP57 | |
| D | ASN117 | |
| D | ILE140 | |
| A | ASP57 | |
| D | MET251 | |
| A | ASN117 | |
| A | ILE140 | |
| A | MET251 | |
| B | GLY31 | |
| B | ASP57 | |
| B | ASN117 | |
| B | ILE140 |
| 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 | ARG104 | |
| C | ARG110 | |
| C | ASN142 | |
| C | ARG176 | |
| D | ARG104 | |
| D | ARG110 | |
| D | ASN142 | |
| D | ARG176 | |
| A | ARG110 | |
| A | ASN142 | |
| A | ARG176 | |
| B | ARG104 | |
| B | ARG110 | |
| B | ASN142 | |
| B | ARG176 | |
| C | ARG104 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 36 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P08249 |
| Chain | Residue | Details |
| A | LYS78 | |
| B | LYS78 | |
| B | LYS91 | |
| B | LYS185 | |
| B | LYS215 | |
| B | LYS296 | |
| B | LYS307 | |
| B | LYS314 | |
| B | LYS324 | |
| B | LYS335 | |
| C | LYS78 | |
| A | LYS91 | |
| C | LYS91 | |
| C | LYS185 | |
| C | LYS215 | |
| C | LYS296 | |
| C | LYS307 | |
| C | LYS314 | |
| C | LYS324 | |
| C | LYS335 | |
| D | LYS78 | |
| D | LYS91 | |
| A | LYS185 | |
| D | LYS185 | |
| D | LYS215 | |
| D | LYS296 | |
| D | LYS307 | |
| D | LYS314 | |
| D | LYS324 | |
| D | LYS335 | |
| A | LYS215 | |
| A | LYS296 | |
| A | LYS307 | |
| A | LYS314 | |
| A | LYS324 | |
| A | LYS335 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS165 | |
| B | LYS165 | |
| C | LYS165 | |
| D | LYS165 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | MOD_RES: N6-succinyllysine => ECO:0000250|UniProtKB:P08249 |
| Chain | Residue | Details |
| A | LYS203 | |
| A | LYS269 | |
| B | LYS203 | |
| B | LYS269 | |
| C | LYS203 | |
| C | LYS269 | |
| D | LYS203 | |
| D | LYS269 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:Q32LG3 |
| Chain | Residue | Details |
| A | LYS239 | |
| D | LYS239 | |
| D | LYS301 | |
| D | LYS328 | |
| A | LYS301 | |
| A | LYS328 | |
| B | LYS239 | |
| B | LYS301 | |
| B | LYS328 | |
| C | LYS239 | |
| C | LYS301 | |
| C | LYS328 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER246 | |
| A | SER326 | |
| B | SER246 | |
| B | SER326 | |
| C | SER246 | |
| C | SER326 | |
| D | SER246 | |
| D | SER326 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-malonyllysine; alternate => ECO:0000250|UniProtKB:Q32LG3 |
| Chain | Residue | Details |
| A | LYS329 | |
| B | LYS329 | |
| C | LYS329 | |
| D | LYS329 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P04636 |
| Chain | Residue | Details |
| A | SER33 | |
| B | SER33 | |
| C | SER33 | |
| D | SER33 |
