4WLN
Crystal structure of apo 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 | 8 |
Details | binding site for residue PO4 A 401 |
Chain | Residue |
A | PRO103 |
A | ARG104 |
A | ARG110 |
A | ASN142 |
A | SER246 |
A | PO4402 |
A | PO4403 |
A | HOH525 |
site_id | AC2 |
Number of Residues | 7 |
Details | binding site for residue PO4 A 402 |
Chain | Residue |
A | PRO99 |
A | ALA100 |
A | ASN117 |
A | ILE140 |
A | ASN142 |
A | PO4401 |
A | ILE36 |
site_id | AC3 |
Number of Residues | 10 |
Details | binding site for residue PO4 A 403 |
Chain | Residue |
A | ARG104 |
A | ARG110 |
A | ASN142 |
A | LEU172 |
A | ARG176 |
A | HIS200 |
A | GLY234 |
A | PO4401 |
A | HOH513 |
A | HOH525 |
site_id | AC4 |
Number of Residues | 10 |
Details | binding site for residue PO4 B 401 |
Chain | Residue |
B | ARG104 |
B | ARG110 |
B | ASN142 |
B | LEU172 |
B | ARG176 |
B | HIS200 |
B | GLY234 |
B | ALA247 |
B | PO4403 |
B | HOH522 |
site_id | AC5 |
Number of Residues | 9 |
Details | binding site for residue PO4 B 402 |
Chain | Residue |
B | PRO99 |
B | ALA100 |
B | GLY101 |
B | VAL102 |
B | ASN117 |
B | ILE140 |
B | ALA141 |
B | ASN142 |
B | PO4403 |
site_id | AC6 |
Number of Residues | 8 |
Details | binding site for residue PO4 B 403 |
Chain | Residue |
B | PRO103 |
B | ARG104 |
B | ARG110 |
B | ASN142 |
B | SER246 |
B | PO4401 |
B | PO4402 |
B | HOH522 |
site_id | AC7 |
Number of Residues | 9 |
Details | binding site for residue PO4 C 401 |
Chain | Residue |
C | ARG104 |
C | ARG110 |
C | ASN142 |
C | LEU172 |
C | ARG176 |
C | HIS200 |
C | GLY234 |
C | ALA247 |
C | PO4402 |
site_id | AC8 |
Number of Residues | 7 |
Details | binding site for residue PO4 C 402 |
Chain | Residue |
C | PRO103 |
C | ARG104 |
C | ARG110 |
C | ASN142 |
C | SER246 |
C | PO4401 |
C | PO4403 |
site_id | AC9 |
Number of Residues | 9 |
Details | binding site for residue PO4 C 403 |
Chain | Residue |
C | ILE36 |
C | PRO99 |
C | ALA100 |
C | VAL102 |
C | PRO103 |
C | ASN117 |
C | ALA141 |
C | ASN142 |
C | PO4402 |
site_id | AD1 |
Number of Residues | 9 |
Details | binding site for residue PO4 D 401 |
Chain | Residue |
D | PRO99 |
D | ALA100 |
D | GLY101 |
D | ASN117 |
D | ILE140 |
D | ALA141 |
D | ASN142 |
D | PO4402 |
D | HOH522 |
site_id | AD2 |
Number of Residues | 8 |
Details | binding site for residue PO4 D 402 |
Chain | Residue |
D | PRO103 |
D | ARG104 |
D | ARG110 |
D | ASN142 |
D | SER246 |
D | PO4401 |
D | PO4403 |
D | HOH522 |
site_id | AD3 |
Number of Residues | 10 |
Details | binding site for residue PO4 D 403 |
Chain | Residue |
D | HIS200 |
D | GLY234 |
D | ALA247 |
D | PO4402 |
D | HOH509 |
D | ARG104 |
D | ARG110 |
D | ASN142 |
D | LEU172 |
D | ARG176 |
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 |