5W8I
Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 23 and Zinc
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0003824 | molecular_function | catalytic activity |
| A | 0004459 | molecular_function | L-lactate dehydrogenase 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 | 0006090 | biological_process | pyruvate 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 | 0019752 | biological_process | carboxylic acid metabolic process |
| A | 0042802 | molecular_function | identical protein binding |
| 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 | 0004459 | molecular_function | L-lactate dehydrogenase 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 | 0006090 | biological_process | pyruvate 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 | 0019752 | biological_process | carboxylic acid metabolic process |
| B | 0042802 | molecular_function | identical protein binding |
| 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 | 0004459 | molecular_function | L-lactate dehydrogenase 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 | 0006090 | biological_process | pyruvate 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 | 0019752 | biological_process | carboxylic acid metabolic process |
| C | 0042802 | molecular_function | identical protein binding |
| 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 | 0004459 | molecular_function | L-lactate dehydrogenase 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 | 0006090 | biological_process | pyruvate 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 | 0019752 | biological_process | carboxylic acid metabolic process |
| D | 0042802 | molecular_function | identical protein binding |
| 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 | 3 |
| Details | binding site for residue ZN A 401 |
| Chain | Residue |
| A | HIS192 |
| A | 9YD403 |
| A | HOH684 |
| site_id | AC2 |
| Number of Residues | 2 |
| Details | binding site for residue ZN A 402 |
| Chain | Residue |
| A | CIT404 |
| C | CIT403 |
| site_id | AC3 |
| Number of Residues | 9 |
| Details | binding site for residue 9YD A 403 |
| Chain | Residue |
| A | ARG168 |
| A | HIS192 |
| A | THR247 |
| A | ZN401 |
| A | HOH567 |
| A | GLN99 |
| A | ARG105 |
| A | LEU108 |
| A | ASN137 |
| site_id | AC4 |
| Number of Residues | 15 |
| Details | binding site for residue CIT A 404 |
| Chain | Residue |
| A | ARG170 |
| A | LEU182 |
| A | ARG268 |
| A | VAL269 |
| A | ZN402 |
| A | HOH509 |
| A | HOH511 |
| A | HOH534 |
| A | HOH626 |
| A | HOH651 |
| C | LEU182 |
| C | SER183 |
| C | HIS185 |
| C | CIT403 |
| C | HOH553 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue DMS A 405 |
| Chain | Residue |
| A | ASN163 |
| A | SER166 |
| A | ARG170 |
| A | HOH506 |
| B | LEU69 |
| 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 | HOH568 |
| site_id | AC7 |
| Number of Residues | 14 |
| Details | binding site for residue CIT B 402 |
| Chain | Residue |
| B | ARG170 |
| B | LEU182 |
| B | ARG268 |
| B | VAL269 |
| B | HOH532 |
| B | HOH600 |
| B | HOH659 |
| C | HOH502 |
| D | LEU182 |
| D | SER183 |
| D | HIS185 |
| D | ZN401 |
| D | CIT404 |
| D | HOH503 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue DMS B 403 |
| Chain | Residue |
| A | LEU69 |
| B | ASN163 |
| B | SER166 |
| B | ARG170 |
| B | HOH503 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | binding site for residue GOL B 404 |
| Chain | Residue |
| B | SER201 |
| B | MET203 |
| B | ASN204 |
| B | GLY207 |
| B | SER209 |
| D | SER201 |
| D | GLY202 |
| D | GLY207 |
| D | SER209 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue ZN C 401 |
| Chain | Residue |
| C | HIS192 |
| C | 9YD402 |
| C | HOH668 |
| site_id | AD2 |
| Number of Residues | 10 |
| Details | binding site for residue 9YD C 402 |
| Chain | Residue |
| C | GLN99 |
| C | ARG105 |
| C | LEU108 |
| C | ASN137 |
| C | ARG168 |
| C | HIS192 |
| C | THR247 |
| C | ZN401 |
| C | HOH597 |
| C | HOH668 |
| site_id | AD3 |
| Number of Residues | 15 |
| Details | binding site for residue CIT C 403 |
| Chain | Residue |
| A | LEU182 |
| A | SER183 |
| A | HIS185 |
| A | ZN402 |
| A | CIT404 |
| A | HOH509 |
| A | HOH524 |
| B | HOH511 |
| C | ARG170 |
| C | LEU182 |
| C | ARG268 |
| C | VAL269 |
| C | HOH520 |
| C | HOH610 |
| C | HOH653 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue DMS C 404 |
| Chain | Residue |
| C | SER166 |
| C | ARG170 |
| C | HOH507 |
| C | ASN163 |
| site_id | AD5 |
| Number of Residues | 2 |
| Details | binding site for residue ZN D 401 |
| Chain | Residue |
| B | CIT402 |
| D | CIT404 |
| site_id | AD6 |
| Number of Residues | 3 |
| Details | binding site for residue ZN D 402 |
| Chain | Residue |
| D | HIS192 |
| D | 9YD403 |
| D | HOH687 |
| site_id | AD7 |
| Number of Residues | 10 |
| Details | binding site for residue 9YD D 403 |
| Chain | Residue |
| D | GLN99 |
| D | LEU108 |
| D | ASN137 |
| D | ARG168 |
| D | HIS192 |
| D | ALA237 |
| D | THR247 |
| D | ZN402 |
| D | HOH611 |
| D | HOH640 |
| site_id | AD8 |
| Number of Residues | 15 |
| Details | binding site for residue CIT D 404 |
| Chain | Residue |
| B | LEU182 |
| B | SER183 |
| B | HIS185 |
| B | CIT402 |
| D | ARG170 |
| D | LEU182 |
| D | ARG268 |
| D | VAL269 |
| D | ZN401 |
| D | HOH503 |
| D | HOH504 |
| D | HOH531 |
| D | HOH538 |
| D | HOH620 |
| D | HOH660 |
| site_id | AD9 |
| Number of Residues | 5 |
| Details | binding site for residue DMS D 405 |
| Chain | Residue |
| C | LEU69 |
| D | ASN163 |
| D | SER166 |
| D | ARG170 |
| D | HOH505 |
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 |
