5W8L
Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 59 and NADH
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 | 36 |
| Details | binding site for residue NAI A 401 |
| Chain | Residue |
| A | GLY28 |
| A | ARG98 |
| A | ILE115 |
| A | ILE119 |
| A | VAL135 |
| A | SER136 |
| A | ASN137 |
| A | SER160 |
| A | LEU164 |
| A | HIS192 |
| A | THR247 |
| A | ALA29 |
| A | ILE251 |
| A | 9YA402 |
| A | HOH517 |
| A | HOH523 |
| A | HOH533 |
| A | HOH556 |
| A | HOH558 |
| A | HOH564 |
| A | HOH575 |
| A | HOH588 |
| A | VAL30 |
| A | HOH607 |
| A | HOH614 |
| A | HOH652 |
| A | HOH656 |
| A | HOH664 |
| A | HOH674 |
| A | HOH719 |
| A | ASP51 |
| A | VAL52 |
| A | ILE53 |
| A | THR94 |
| A | ALA95 |
| A | GLY96 |
| site_id | AC2 |
| Number of Residues | 21 |
| Details | binding site for residue 9YA A 402 |
| Chain | Residue |
| A | ARG105 |
| A | VAL109 |
| A | ASN137 |
| A | PRO138 |
| A | VAL139 |
| A | ASP140 |
| A | ILE141 |
| A | LEU164 |
| A | ARG168 |
| A | GLU191 |
| A | HIS192 |
| A | ASP194 |
| A | ALA237 |
| A | TYR238 |
| A | THR247 |
| A | LEU322 |
| A | NAI401 |
| A | EDO404 |
| A | EDO405 |
| A | HOH754 |
| D | GLU328 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 403 |
| Chain | Residue |
| A | LEU11 |
| A | LEU12 |
| A | LYS13 |
| B | LYS125 |
| B | TYR126 |
| B | HOH664 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | ARG105 |
| A | ILE241 |
| A | 9YA402 |
| A | HOH675 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | GLU191 |
| A | THR321 |
| A | LEU322 |
| A | 9YA402 |
| D | GLY324 |
| site_id | AC6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | TYR280 |
| A | LYS304 |
| A | VAL305 |
| site_id | AC7 |
| Number of Residues | 33 |
| Details | binding site for residue NAI B 401 |
| Chain | Residue |
| B | HOH555 |
| B | HOH566 |
| B | HOH584 |
| B | HOH585 |
| B | HOH615 |
| B | HOH632 |
| B | HOH634 |
| B | HOH673 |
| B | HOH711 |
| B | GLY28 |
| B | ALA29 |
| B | VAL30 |
| B | ASP51 |
| B | VAL52 |
| B | ILE53 |
| B | THR94 |
| B | ALA95 |
| B | GLY96 |
| B | ARG98 |
| B | ILE115 |
| B | VAL135 |
| B | SER136 |
| B | ASN137 |
| B | SER160 |
| B | LEU164 |
| B | HIS192 |
| B | THR247 |
| B | ILE251 |
| B | 9YA402 |
| B | HOH505 |
| B | HOH524 |
| B | HOH529 |
| B | HOH550 |
| site_id | AC8 |
| Number of Residues | 20 |
| Details | binding site for residue 9YA B 402 |
| Chain | Residue |
| B | ARG105 |
| B | LEU108 |
| B | ASN137 |
| B | PRO138 |
| B | VAL139 |
| B | ASP140 |
| B | ILE141 |
| B | ARG168 |
| B | GLU191 |
| B | HIS192 |
| B | ASP194 |
| B | ALA237 |
| B | TYR238 |
| B | ILE241 |
| B | THR247 |
| B | LEU322 |
| B | NAI401 |
| B | EDO403 |
| B | HOH684 |
| B | HOH766 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 403 |
| Chain | Residue |
| B | ARG105 |
| B | TYR238 |
| B | ILE241 |
| B | 9YA402 |
| B | HOH543 |
| site_id | AD1 |
| Number of Residues | 34 |
| Details | binding site for residue NAI C 401 |
| Chain | Residue |
| C | GLY28 |
| C | ALA29 |
| C | VAL30 |
| C | ASP51 |
| C | VAL52 |
| C | ILE53 |
| C | THR94 |
| C | ALA95 |
| C | GLY96 |
| C | ARG98 |
| C | ILE115 |
| C | ILE119 |
| C | VAL135 |
| C | SER136 |
| C | ASN137 |
| C | SER160 |
| C | LEU164 |
| C | HIS192 |
| C | THR247 |
| C | ILE251 |
| C | 9YA402 |
| C | HOH502 |
| C | HOH518 |
| C | HOH532 |
| C | HOH550 |
| C | HOH576 |
| C | HOH604 |
| C | HOH613 |
| C | HOH614 |
| C | HOH618 |
| C | HOH643 |
| C | HOH650 |
| C | HOH654 |
| C | HOH678 |
| site_id | AD2 |
| Number of Residues | 18 |
| Details | binding site for residue 9YA C 402 |
| Chain | Residue |
| C | ARG105 |
| C | ASN137 |
| C | PRO138 |
| C | VAL139 |
| C | ASP140 |
| C | ILE141 |
| C | LEU164 |
| C | ARG168 |
| C | GLU191 |
| C | HIS192 |
| C | ASP194 |
| C | ALA237 |
| C | TYR238 |
| C | THR247 |
| C | LEU322 |
| C | NAI401 |
| C | HOH657 |
| C | HOH741 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 403 |
| Chain | Residue |
| C | ARG105 |
| C | ILE241 |
| C | EDO404 |
| C | HOH624 |
| site_id | AD4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 404 |
| Chain | Residue |
| C | TYR238 |
| C | ILE241 |
| C | EDO403 |
| C | HOH513 |
| C | HOH587 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 405 |
| Chain | Residue |
| C | ARG176 |
| C | GLU228 |
| C | VAL229 |
| C | HOH552 |
| site_id | AD6 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 406 |
| Chain | Residue |
| A | LEU69 |
| A | HOH714 |
| C | ASN163 |
| C | ARG170 |
| C | PRO271 |
| C | HOH554 |
| C | HOH560 |
| site_id | AD7 |
| Number of Residues | 34 |
| Details | binding site for residue NAI D 401 |
| Chain | Residue |
| D | GLY28 |
| D | ALA29 |
| D | VAL30 |
| D | ASP51 |
| D | VAL52 |
| D | ILE53 |
| D | THR94 |
| D | ALA95 |
| D | GLY96 |
| D | ARG98 |
| D | ILE115 |
| D | ILE119 |
| D | VAL135 |
| D | SER136 |
| D | ASN137 |
| D | SER160 |
| D | LEU164 |
| D | HIS192 |
| D | THR247 |
| D | ILE251 |
| D | 9YA402 |
| D | HOH508 |
| D | HOH518 |
| D | HOH520 |
| D | HOH540 |
| D | HOH551 |
| D | HOH553 |
| D | HOH563 |
| D | HOH572 |
| D | HOH585 |
| D | HOH593 |
| D | HOH598 |
| D | HOH626 |
| D | HOH641 |
| site_id | AD8 |
| Number of Residues | 19 |
| Details | binding site for residue 9YA D 402 |
| Chain | Residue |
| A | GLU328 |
| D | ARG105 |
| D | ASN137 |
| D | PRO138 |
| D | VAL139 |
| D | ASP140 |
| D | ILE141 |
| D | ARG168 |
| D | GLU191 |
| D | HIS192 |
| D | ASP194 |
| D | ALA237 |
| D | TYR238 |
| D | ILE241 |
| D | THR247 |
| D | LEU322 |
| D | NAI401 |
| D | EDO403 |
| D | EDO406 |
| site_id | AD9 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 403 |
| Chain | Residue |
| D | ARG105 |
| D | ILE241 |
| D | 9YA402 |
| D | HOH675 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 404 |
| Chain | Residue |
| D | ARG176 |
| D | GLU228 |
| D | VAL229 |
| D | HOH544 |
| site_id | AE2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO D 405 |
| Chain | Residue |
| A | TRP323 |
| D | SER195 |
| D | ARG314 |
| D | HOH552 |
| D | HOH672 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 406 |
| Chain | Residue |
| A | GLY324 |
| D | GLU191 |
| D | THR321 |
| D | LEU322 |
| D | ILE325 |
| D | 9YA402 |
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 |
