5W8H
Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004457 | molecular_function | lactate dehydrogenase activity |
| A | 0004459 | molecular_function | L-lactate dehydrogenase (NAD+) activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005829 | cellular_component | cytosol |
| A | 0006089 | biological_process | lactate metabolic process |
| A | 0006096 | biological_process | glycolytic process |
| A | 0016020 | cellular_component | membrane |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0019661 | biological_process | glucose catabolic process to lactate via pyruvate |
| A | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0035686 | cellular_component | sperm fibrous sheath |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0042867 | biological_process | pyruvate catabolic process |
| A | 0045296 | molecular_function | cadherin binding |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 1990204 | cellular_component | oxidoreductase complex |
| B | 0003824 | molecular_function | catalytic activity |
| B | 0004457 | molecular_function | lactate dehydrogenase activity |
| B | 0004459 | molecular_function | L-lactate dehydrogenase (NAD+) activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005829 | cellular_component | cytosol |
| B | 0006089 | biological_process | lactate metabolic process |
| B | 0006096 | biological_process | glycolytic process |
| B | 0016020 | cellular_component | membrane |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0019661 | biological_process | glucose catabolic process to lactate via pyruvate |
| B | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0035686 | cellular_component | sperm fibrous sheath |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0042867 | biological_process | pyruvate catabolic process |
| B | 0045296 | molecular_function | cadherin binding |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 1990204 | cellular_component | oxidoreductase complex |
| C | 0003824 | molecular_function | catalytic activity |
| C | 0004457 | molecular_function | lactate dehydrogenase activity |
| C | 0004459 | molecular_function | L-lactate dehydrogenase (NAD+) activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005829 | cellular_component | cytosol |
| C | 0006089 | biological_process | lactate metabolic process |
| C | 0006096 | biological_process | glycolytic process |
| C | 0016020 | cellular_component | membrane |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| C | 0019661 | biological_process | glucose catabolic process to lactate via pyruvate |
| C | 0019752 | biological_process | carboxylic acid metabolic process |
| C | 0035686 | cellular_component | sperm fibrous sheath |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0042867 | biological_process | pyruvate catabolic process |
| C | 0045296 | molecular_function | cadherin binding |
| C | 0070062 | cellular_component | extracellular exosome |
| C | 1990204 | cellular_component | oxidoreductase complex |
| D | 0003824 | molecular_function | catalytic activity |
| D | 0004457 | molecular_function | lactate dehydrogenase activity |
| D | 0004459 | molecular_function | L-lactate dehydrogenase (NAD+) activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005829 | cellular_component | cytosol |
| D | 0006089 | biological_process | lactate metabolic process |
| D | 0006096 | biological_process | glycolytic process |
| D | 0016020 | cellular_component | membrane |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| D | 0019661 | biological_process | glucose catabolic process to lactate via pyruvate |
| D | 0019752 | biological_process | carboxylic acid metabolic process |
| D | 0035686 | cellular_component | sperm fibrous sheath |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0042867 | biological_process | pyruvate catabolic process |
| D | 0045296 | molecular_function | cadherin binding |
| D | 0070062 | cellular_component | extracellular exosome |
| D | 1990204 | cellular_component | oxidoreductase complex |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 11 |
| Details | binding site for residue 9Y1 A 501 |
| Chain | Residue |
| A | GLN99 |
| A | THR247 |
| A | HOH776 |
| A | LEU108 |
| A | ASN137 |
| A | LEU164 |
| A | ARG168 |
| A | HIS192 |
| A | GLY193 |
| A | ASP194 |
| A | TYR238 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | binding site for residue 9Y1 A 502 |
| Chain | Residue |
| A | VAL25 |
| A | GLY26 |
| A | VAL50 |
| A | ASP51 |
| A | VAL52 |
| A | ALA95 |
| A | ILE115 |
| A | PHE118 |
| A | ILE119 |
| A | HOH616 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue ACT A 503 |
| Chain | Residue |
| A | ARG170 |
| A | HIS185 |
| A | HOH603 |
| A | HOH636 |
| A | HOH653 |
| C | HIS185 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | binding site for residue ACT A 504 |
| Chain | Residue |
| A | LEU182 |
| A | HIS185 |
| A | HOH609 |
| C | ARG170 |
| C | HOH607 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue DMS A 505 |
| Chain | Residue |
| A | THR212 |
| A | LEU213 |
| A | HOH670 |
| B | LYS125 |
| B | TYR126 |
| C | THR306 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | binding site for residue MLA B 401 |
| Chain | Residue |
| B | ARG105 |
| B | ASN137 |
| B | LEU164 |
| B | ARG168 |
| B | HIS192 |
| B | ALA237 |
| B | THR247 |
| B | HOH546 |
| site_id | AC7 |
| Number of Residues | 9 |
| Details | binding site for residue 9Y1 B 402 |
| Chain | Residue |
| B | SER309 |
| B | GLU310 |
| B | ARG314 |
| B | LYS317 |
| B | HOH582 |
| C | 9Y1504 |
| D | LYS117 |
| D | PHE331 |
| D | HOH582 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue ACT B 403 |
| Chain | Residue |
| B | ASP220 |
| B | LYS221 |
| B | ASP222 |
| B | GLN225 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue DMS B 404 |
| Chain | Residue |
| A | LEU69 |
| B | ASN163 |
| B | SER166 |
| B | ARG170 |
| B | VAL269 |
| site_id | AD1 |
| Number of Residues | 10 |
| Details | binding site for residue 9Y1 C 501 |
| Chain | Residue |
| C | GLN99 |
| C | LEU108 |
| C | ASN137 |
| C | ARG168 |
| C | HIS192 |
| C | GLY193 |
| C | ASP194 |
| C | ALA237 |
| C | TYR238 |
| C | THR247 |
| site_id | AD2 |
| Number of Residues | 15 |
| Details | binding site for residue 9Y1 C 502 |
| Chain | Residue |
| C | VAL25 |
| C | GLY26 |
| C | VAL50 |
| C | ASP51 |
| C | VAL52 |
| C | ALA95 |
| C | ASN114 |
| C | ILE115 |
| C | PHE118 |
| C | ILE119 |
| C | HOH605 |
| C | HOH613 |
| C | HOH716 |
| D | GLU101 |
| D | GLY102 |
| site_id | AD3 |
| Number of Residues | 10 |
| Details | binding site for residue 9Y1 C 503 |
| Chain | Residue |
| C | SER104 |
| C | ARG105 |
| C | LEU106 |
| C | ASP320 |
| C | THR321 |
| C | GLY324 |
| C | ILE325 |
| C | GLU328 |
| C | 9Y1504 |
| C | HOH647 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue 9Y1 C 504 |
| Chain | Residue |
| B | 9Y1402 |
| B | HOH567 |
| C | 9Y1503 |
| C | HOH647 |
| site_id | AD5 |
| Number of Residues | 9 |
| Details | binding site for residue GOL C 505 |
| Chain | Residue |
| A | SER201 |
| A | GLY202 |
| A | GLY207 |
| C | SER201 |
| C | GLY202 |
| C | MET203 |
| C | ASN204 |
| C | GLY207 |
| C | SER209 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue ACT D 401 |
| Chain | Residue |
| D | PRO128 |
| D | LEU307 |
| D | GLU312 |
| site_id | AD7 |
| Number of Residues | 4 |
| Details | binding site for residue DMS D 402 |
| Chain | Residue |
| D | GLY96 |
| D | ALA97 |
| D | SER136 |
| D | ASN137 |
| site_id | AD8 |
| Number of Residues | 11 |
| Details | binding site for residue GOL D 403 |
| Chain | Residue |
| B | SER201 |
| B | GLY202 |
| B | ASN204 |
| B | GLY207 |
| B | SER209 |
| D | SER201 |
| D | GLY202 |
| D | MET203 |
| D | ASN204 |
| D | GLY207 |
| D | SER209 |
Functional Information from PROSITE/UniProt
| site_id | PS00064 |
| Number of Residues | 7 |
| Details | L_LDH L-lactate dehydrogenase active site. LGEHGDS |
| Chain | Residue | Details |
| A | LEU189-SER195 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: Proton acceptor |
| Chain | Residue | Details |
| A | HIS192 | |
| B | HIS192 | |
| C | HIS192 | |
| D | HIS192 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:11276087 |
| Chain | Residue | Details |
| A | GLY28 | |
| A | ARG98 | |
| B | GLY28 | |
| B | ARG98 | |
| C | GLY28 | |
| C | ARG98 | |
| D | GLY28 | |
| D | ARG98 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | ARG105 | |
| C | ASN137 | |
| C | ARG168 | |
| C | THR247 | |
| D | ARG105 | |
| D | ASN137 | |
| D | ARG168 | |
| D | THR247 | |
| A | ASN137 | |
| A | ARG168 | |
| A | THR247 | |
| B | ARG105 | |
| B | ASN137 | |
| B | ARG168 | |
| B | THR247 | |
| C | ARG105 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: N-acetylalanine => ECO:0000269|Ref.10, ECO:0007744|PubMed:19413330, ECO:0007744|PubMed:22223895 |
| Chain | Residue | Details |
| A | ALA1 | |
| B | ALA1 | |
| C | ALA1 | |
| D | ALA1 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P06151 |
| Chain | Residue | Details |
| A | LYS4 | |
| D | LYS4 | |
| D | LYS117 | |
| D | LYS317 | |
| A | LYS117 | |
| A | LYS317 | |
| B | LYS4 | |
| B | LYS117 | |
| B | LYS317 | |
| C | LYS4 | |
| C | LYS117 | |
| C | LYS317 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | TYR9 | |
| B | TYR9 | |
| C | TYR9 | |
| D | TYR9 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS13 | |
| D | LYS13 | |
| D | LYS80 | |
| D | LYS125 | |
| A | LYS80 | |
| A | LYS125 | |
| B | LYS13 | |
| B | LYS80 | |
| B | LYS125 | |
| C | LYS13 | |
| C | LYS80 | |
| C | LYS125 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | THR17 | |
| B | THR17 | |
| C | THR17 | |
| D | THR17 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS56 | |
| B | LYS56 | |
| C | LYS56 | |
| D | LYS56 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 12 |
| Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P06151 |
| Chain | Residue | Details |
| A | LYS223 | |
| D | LYS223 | |
| D | LYS231 | |
| D | LYS242 | |
| A | LYS231 | |
| A | LYS242 | |
| B | LYS223 | |
| B | LYS231 | |
| B | LYS242 | |
| C | LYS223 | |
| C | LYS231 | |
| C | LYS242 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P06151 |
| Chain | Residue | Details |
| A | TYR238 | |
| B | TYR238 | |
| C | TYR238 | |
| D | TYR238 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 8 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04642 |
| Chain | Residue | Details |
| A | THR308 | |
| A | THR321 | |
| B | THR308 | |
| B | THR321 | |
| C | THR308 | |
| C | THR321 | |
| D | THR308 | |
| D | THR321 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
| Chain | Residue | Details |
| A | SER309 | |
| B | SER309 | |
| C | SER309 | |
| D | SER309 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 8 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| A | LYS56 | |
| B | LYS56 | |
| C | LYS56 | |
| D | LYS56 |
