6Q0D
CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION
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 |
E | 0003824 | molecular_function | catalytic activity |
E | 0004459 | molecular_function | L-lactate dehydrogenase activity |
E | 0005515 | molecular_function | protein binding |
E | 0005634 | cellular_component | nucleus |
E | 0005737 | cellular_component | cytoplasm |
E | 0005739 | cellular_component | mitochondrion |
E | 0005829 | cellular_component | cytosol |
E | 0006089 | biological_process | lactate metabolic process |
E | 0006090 | biological_process | pyruvate metabolic process |
E | 0006096 | biological_process | glycolytic process |
E | 0016020 | cellular_component | membrane |
E | 0016491 | molecular_function | oxidoreductase activity |
E | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
E | 0019752 | biological_process | carboxylic acid metabolic process |
E | 0042802 | molecular_function | identical protein binding |
E | 0045296 | molecular_function | cadherin binding |
E | 0070062 | cellular_component | extracellular exosome |
E | 1990204 | cellular_component | oxidoreductase complex |
F | 0003824 | molecular_function | catalytic activity |
F | 0004459 | molecular_function | L-lactate dehydrogenase activity |
F | 0005515 | molecular_function | protein binding |
F | 0005634 | cellular_component | nucleus |
F | 0005737 | cellular_component | cytoplasm |
F | 0005739 | cellular_component | mitochondrion |
F | 0005829 | cellular_component | cytosol |
F | 0006089 | biological_process | lactate metabolic process |
F | 0006090 | biological_process | pyruvate metabolic process |
F | 0006096 | biological_process | glycolytic process |
F | 0016020 | cellular_component | membrane |
F | 0016491 | molecular_function | oxidoreductase activity |
F | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
F | 0019752 | biological_process | carboxylic acid metabolic process |
F | 0042802 | molecular_function | identical protein binding |
F | 0045296 | molecular_function | cadherin binding |
F | 0070062 | cellular_component | extracellular exosome |
F | 1990204 | cellular_component | oxidoreductase complex |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 7 |
Details | binding site for residue PO4 A 501 |
Chain | Residue |
A | ARG170 |
A | HIS185 |
A | HOH613 |
A | HOH617 |
A | HOH652 |
C | HIS185 |
C | HOH626 |
site_id | AC2 |
Number of Residues | 16 |
Details | binding site for residue P8M A 502 |
Chain | Residue |
A | ASN137 |
A | PRO138 |
A | VAL139 |
A | ASP140 |
A | ILE141 |
A | ARG168 |
A | GLU191 |
A | HIS192 |
A | GLY193 |
A | ASP194 |
A | ALA237 |
A | THR247 |
A | LEU322 |
A | NAI503 |
A | ARG105 |
A | LEU108 |
site_id | AC3 |
Number of Residues | 28 |
Details | binding site for residue NAI A 503 |
Chain | Residue |
A | GLY28 |
A | ALA29 |
A | VAL30 |
A | ASP51 |
A | VAL52 |
A | ILE53 |
A | THR94 |
A | ALA95 |
A | GLY96 |
A | ARG98 |
A | ILE115 |
A | ILE119 |
A | VAL135 |
A | SER136 |
A | ASN137 |
A | HIS192 |
A | THR247 |
A | ILE251 |
A | P8M502 |
A | HOH609 |
A | HOH612 |
A | HOH619 |
A | HOH636 |
A | HOH637 |
A | HOH646 |
A | HOH663 |
A | HOH666 |
A | HOH687 |
site_id | AC4 |
Number of Residues | 5 |
Details | binding site for residue GOL B 500 |
Chain | Residue |
B | SER78 |
B | GLY79 |
B | HOH612 |
B | HOH620 |
B | HOH645 |
site_id | AC5 |
Number of Residues | 7 |
Details | binding site for residue PO4 B 501 |
Chain | Residue |
B | ARG170 |
B | HIS185 |
B | HOH669 |
B | HOH672 |
B | HOH674 |
D | HIS185 |
D | HOH630 |
site_id | AC6 |
Number of Residues | 16 |
Details | binding site for residue P8M B 502 |
Chain | Residue |
B | LEU108 |
B | ASN137 |
B | PRO138 |
B | VAL139 |
B | ASP140 |
B | ILE141 |
B | LEU164 |
B | ARG168 |
B | GLU191 |
B | HIS192 |
B | TYR238 |
B | THR247 |
B | LEU322 |
B | ILE325 |
B | NAI503 |
E | GLU328 |
site_id | AC7 |
Number of Residues | 25 |
Details | binding site for residue NAI B 503 |
Chain | Residue |
B | HOH627 |
B | HOH648 |
B | HOH650 |
B | HOH670 |
B | HOH692 |
B | GLY28 |
B | ALA29 |
B | VAL30 |
B | ASP51 |
B | VAL52 |
B | ILE53 |
B | THR94 |
B | ALA95 |
B | GLY96 |
B | ILE115 |
B | ILE119 |
B | VAL135 |
B | SER136 |
B | ASN137 |
B | HIS192 |
B | THR247 |
B | ILE251 |
B | P8M502 |
B | HOH611 |
B | HOH622 |
site_id | AC8 |
Number of Residues | 5 |
Details | binding site for residue GOL C 500 |
Chain | Residue |
C | GLU54 |
C | SER78 |
C | GLY79 |
C | LYS80 |
C | ASP81 |
site_id | AC9 |
Number of Residues | 7 |
Details | binding site for residue PO4 C 501 |
Chain | Residue |
A | HIS185 |
A | HOH620 |
C | ARG170 |
C | HIS185 |
C | HOH602 |
C | HOH648 |
C | HOH665 |
site_id | AD1 |
Number of Residues | 19 |
Details | binding site for residue P8M C 502 |
Chain | Residue |
C | ARG105 |
C | LEU106 |
C | VAL109 |
C | ASN137 |
C | PRO138 |
C | VAL139 |
C | ASP140 |
C | ILE141 |
C | ARG168 |
C | GLU191 |
C | HIS192 |
C | GLY193 |
C | ILE241 |
C | THR247 |
C | LEU322 |
C | ILE325 |
C | NAI503 |
C | HOH633 |
F | GLU328 |
site_id | AD2 |
Number of Residues | 25 |
Details | binding site for residue NAI C 503 |
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 | ASN137 |
C | LEU164 |
C | HIS192 |
C | THR247 |
C | ILE251 |
C | P8M502 |
C | HOH601 |
C | HOH603 |
C | HOH624 |
C | HOH630 |
C | HOH649 |
C | HOH651 |
site_id | AD3 |
Number of Residues | 7 |
Details | binding site for residue PO4 D 501 |
Chain | Residue |
B | HIS185 |
B | HOH647 |
D | ARG170 |
D | HIS185 |
D | HOH613 |
D | HOH621 |
D | HOH653 |
site_id | AD4 |
Number of Residues | 19 |
Details | binding site for residue P8M D 502 |
Chain | Residue |
D | ARG105 |
D | LEU108 |
D | VAL109 |
D | ASN137 |
D | PRO138 |
D | VAL139 |
D | ASP140 |
D | ILE141 |
D | LEU164 |
D | ARG168 |
D | GLU191 |
D | HIS192 |
D | ALA237 |
D | TYR238 |
D | THR247 |
D | LEU322 |
D | ILE325 |
D | NAI503 |
D | HOH682 |
site_id | AD5 |
Number of Residues | 24 |
Details | binding site for residue NAI D 503 |
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 | HIS192 |
D | THR247 |
D | ILE251 |
D | P8M502 |
D | HOH609 |
D | HOH615 |
D | HOH646 |
D | HOH651 |
D | HOH660 |
site_id | AD6 |
Number of Residues | 6 |
Details | binding site for residue GOL E 401 |
Chain | Residue |
E | PRO198 |
E | TRP200 |
E | THR308 |
E | GLU310 |
E | GLU311 |
E | ARG314 |
site_id | AD7 |
Number of Residues | 2 |
Details | binding site for residue GOL E 402 |
Chain | Residue |
E | LYS41 |
E | HOH517 |
site_id | AD8 |
Number of Residues | 5 |
Details | binding site for residue GOL E 403 |
Chain | Residue |
E | ASP5 |
E | ILE8 |
E | TYR9 |
E | ASN10 |
F | LYS304 |
site_id | AD9 |
Number of Residues | 9 |
Details | binding site for residue PO4 E 404 |
Chain | Residue |
E | ARG170 |
E | HIS185 |
E | HOH513 |
E | HOH531 |
E | HOH538 |
E | HOH550 |
E | HOH551 |
F | HIS185 |
F | HOH613 |
site_id | AE1 |
Number of Residues | 20 |
Details | binding site for residue P8M E 405 |
Chain | Residue |
B | GLU328 |
E | ARG105 |
E | LEU106 |
E | LEU108 |
E | VAL109 |
E | ASN137 |
E | PRO138 |
E | VAL139 |
E | ASP140 |
E | ILE141 |
E | LEU164 |
E | ARG168 |
E | GLU191 |
E | HIS192 |
E | THR247 |
E | LEU322 |
E | ILE325 |
E | NAI406 |
E | HOH599 |
E | HOH612 |
site_id | AE2 |
Number of Residues | 31 |
Details | binding site for residue NAI E 406 |
Chain | Residue |
E | GLY28 |
E | ALA29 |
E | VAL30 |
E | ASP51 |
E | VAL52 |
E | ILE53 |
E | THR94 |
E | ALA95 |
E | GLY96 |
E | ARG98 |
E | ILE115 |
E | ILE119 |
E | VAL135 |
E | SER136 |
E | ASN137 |
E | LEU164 |
E | HIS192 |
E | THR247 |
E | ILE251 |
E | P8M405 |
E | HOH506 |
E | HOH507 |
E | HOH510 |
E | HOH524 |
E | HOH532 |
E | HOH536 |
E | HOH540 |
E | HOH586 |
E | HOH593 |
E | HOH600 |
E | HOH626 |
site_id | AE3 |
Number of Residues | 1 |
Details | binding site for residue GOL F 500 |
Chain | Residue |
F | ALA313 |
site_id | AE4 |
Number of Residues | 9 |
Details | binding site for residue PO4 F 501 |
Chain | Residue |
E | HIS185 |
E | HOH534 |
F | ARG170 |
F | HIS185 |
F | HOH606 |
F | HOH642 |
F | HOH645 |
F | HOH655 |
F | HOH727 |
site_id | AE5 |
Number of Residues | 16 |
Details | binding site for residue P8M F 502 |
Chain | Residue |
C | GLU328 |
F | LEU108 |
F | VAL109 |
F | ASN137 |
F | PRO138 |
F | VAL139 |
F | ASP140 |
F | ILE141 |
F | LEU164 |
F | ARG168 |
F | GLU191 |
F | HIS192 |
F | THR247 |
F | LEU322 |
F | NAI503 |
F | HOH722 |
site_id | AE6 |
Number of Residues | 32 |
Details | binding site for residue NAI F 503 |
Chain | Residue |
F | GLY28 |
F | ALA29 |
F | VAL30 |
F | ASP51 |
F | VAL52 |
F | ILE53 |
F | THR94 |
F | ALA95 |
F | GLY96 |
F | ARG98 |
F | ILE115 |
F | PHE118 |
F | ILE119 |
F | VAL135 |
F | SER136 |
F | ASN137 |
F | HIS192 |
F | THR247 |
F | ILE251 |
F | P8M502 |
F | HOH603 |
F | HOH604 |
F | HOH615 |
F | HOH630 |
F | HOH643 |
F | HOH644 |
F | HOH656 |
F | HOH662 |
F | HOH678 |
F | HOH693 |
F | HOH705 |
F | HOH712 |
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 | 6 |
Details | ACT_SITE: Proton acceptor |
Chain | Residue | Details |
A | HIS192 | |
B | HIS192 | |
C | HIS192 | |
D | HIS192 | |
E | HIS192 | |
F | HIS192 |
site_id | SWS_FT_FI2 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11276087 |
Chain | Residue | Details |
D | GLY28 | |
D | ARG98 | |
E | GLY28 | |
E | ARG98 | |
F | GLY28 | |
F | ARG98 | |
A | GLY28 | |
A | ARG98 | |
B | GLY28 | |
B | ARG98 | |
C | GLY28 | |
C | ARG98 |
site_id | SWS_FT_FI3 |
Number of Residues | 24 |
Details | BINDING: |
Chain | Residue | Details |
B | ARG168 | |
B | THR247 | |
C | ARG105 | |
C | ASN137 | |
C | ARG168 | |
C | THR247 | |
D | ARG105 | |
D | ASN137 | |
D | ARG168 | |
D | THR247 | |
E | ARG105 | |
E | ASN137 | |
E | ARG168 | |
E | THR247 | |
F | ARG105 | |
F | ASN137 | |
F | ARG168 | |
F | THR247 | |
A | ARG105 | |
A | ASN137 | |
A | ARG168 | |
A | THR247 | |
B | ARG105 | |
B | ASN137 |
site_id | SWS_FT_FI4 |
Number of Residues | 6 |
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 | |
E | ALA1 | |
F | ALA1 |
site_id | SWS_FT_FI5 |
Number of Residues | 18 |
Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000250|UniProtKB:P06151 |
Chain | Residue | Details |
C | LYS4 | |
C | LYS117 | |
C | LYS317 | |
D | LYS4 | |
D | LYS117 | |
D | LYS317 | |
E | LYS4 | |
E | LYS117 | |
E | LYS317 | |
F | LYS4 | |
F | LYS117 | |
F | LYS317 | |
A | LYS4 | |
A | LYS117 | |
A | LYS317 | |
B | LYS4 | |
B | LYS117 | |
B | LYS317 |
site_id | SWS_FT_FI6 |
Number of Residues | 6 |
Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:19690332 |
Chain | Residue | Details |
A | TYR9 | |
B | TYR9 | |
C | TYR9 | |
D | TYR9 | |
E | TYR9 | |
F | TYR9 |
site_id | SWS_FT_FI7 |
Number of Residues | 18 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
C | LYS13 | |
C | LYS80 | |
C | LYS125 | |
D | LYS13 | |
D | LYS80 | |
D | LYS125 | |
E | LYS13 | |
E | LYS80 | |
E | LYS125 | |
F | LYS13 | |
F | LYS80 | |
F | LYS125 | |
B | LYS80 | |
B | LYS125 | |
A | LYS13 | |
A | LYS80 | |
A | LYS125 | |
B | LYS13 |
site_id | SWS_FT_FI8 |
Number of Residues | 6 |
Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
F | THR17 | |
A | THR17 | |
B | THR17 | |
C | THR17 | |
D | THR17 | |
E | THR17 |
site_id | SWS_FT_FI9 |
Number of Residues | 6 |
Details | MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
E | LYS56 | |
F | LYS56 | |
A | LYS56 | |
B | LYS56 | |
C | LYS56 | |
D | LYS56 |
site_id | SWS_FT_FI10 |
Number of Residues | 18 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P06151 |
Chain | Residue | Details |
C | LYS223 | |
C | LYS231 | |
C | LYS242 | |
D | LYS223 | |
D | LYS231 | |
D | LYS242 | |
E | LYS223 | |
E | LYS231 | |
E | LYS242 | |
F | LYS223 | |
F | LYS231 | |
F | LYS242 | |
A | LYS223 | |
A | LYS231 | |
A | LYS242 | |
B | LYS223 | |
B | LYS231 | |
B | LYS242 |
site_id | SWS_FT_FI11 |
Number of Residues | 6 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P06151 |
Chain | Residue | Details |
A | TYR238 | |
B | TYR238 | |
C | TYR238 | |
D | TYR238 | |
E | TYR238 | |
F | TYR238 |
site_id | SWS_FT_FI12 |
Number of Residues | 12 |
Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04642 |
Chain | Residue | Details |
D | THR308 | |
D | THR321 | |
E | THR308 | |
E | THR321 | |
F | THR308 | |
F | THR321 | |
A | THR321 | |
B | THR321 | |
C | THR321 | |
A | THR308 | |
B | THR308 | |
C | THR308 |
site_id | SWS_FT_FI13 |
Number of Residues | 6 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163, ECO:0007744|PubMed:24275569 |
Chain | Residue | Details |
A | SER309 | |
B | SER309 | |
C | SER309 | |
D | SER309 | |
E | SER309 | |
F | SER309 |
site_id | SWS_FT_FI14 |
Number of Residues | 12 |
Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0007744|PubMed:28112733 |
Chain | Residue | Details |
D | LYS56 | |
E | LYS56 | |
F | LYS56 | |
A | LYS56 | |
B | LYS56 | |
C | LYS56 |