3KB6
Crystal structure of D-Lactate dehydrogenase from aquifex aeolicus complexed with NAD and Lactic acid
Replaces: 2PI1Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| A | 0006564 | biological_process | L-serine biosynthetic process |
| A | 0008720 | molecular_function | D-lactate dehydrogenase (NAD+) activity |
| 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 | 0051287 | molecular_function | NAD binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| B | 0006564 | biological_process | L-serine biosynthetic process |
| B | 0008720 | molecular_function | D-lactate dehydrogenase (NAD+) activity |
| 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 | 0051287 | molecular_function | NAD binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| C | 0006564 | biological_process | L-serine biosynthetic process |
| C | 0008720 | molecular_function | D-lactate dehydrogenase (NAD+) activity |
| 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 | 0051287 | molecular_function | NAD binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0004617 | molecular_function | phosphoglycerate dehydrogenase activity |
| D | 0006564 | biological_process | L-serine biosynthetic process |
| D | 0008720 | molecular_function | D-lactate dehydrogenase (NAD+) activity |
| 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 | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PPI A 398 |
| Chain | Residue |
| A | PRO9 |
| A | ARG71 |
| A | TYR297 |
| A | HOH450 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE LAC A 399 |
| Chain | Residue |
| A | ARG231 |
| A | HIS294 |
| A | NAD400 |
| A | PHE49 |
| A | SER72 |
| A | VAL73 |
| A | GLY74 |
| A | TYR96 |
| site_id | AC3 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE NAD A 400 |
| Chain | Residue |
| A | VAL73 |
| A | TYR96 |
| A | VAL101 |
| A | GLY150 |
| A | ARG151 |
| A | ILE152 |
| A | TYR170 |
| A | ASP171 |
| A | VAL172 |
| A | HIS201 |
| A | PRO203 |
| A | THR208 |
| A | THR229 |
| A | ALA230 |
| A | ARG231 |
| A | ASP255 |
| A | HIS294 |
| A | ALA296 |
| A | TYR297 |
| A | LAC399 |
| A | HOH405 |
| A | HOH406 |
| A | HOH407 |
| A | HOH416 |
| A | HOH417 |
| A | HOH437 |
| A | HOH449 |
| A | HOH471 |
| A | PEG701 |
| A | GOL710 |
| C | HOH408 |
| C | HOH462 |
| C | PEG702 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PEG A 403 |
| Chain | Residue |
| A | ARG137 |
| A | ASP196 |
| A | ASP222 |
| A | GLY223 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE 1PE A 404 |
| Chain | Residue |
| A | ASP171 |
| A | VAL172 |
| A | LYS174 |
| A | THR186 |
| A | HOH426 |
| C | GLU190 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PPI A 453 |
| Chain | Residue |
| A | VAL50 |
| A | TYR51 |
| A | ASP76 |
| A | ARG231 |
| A | GLU260 |
| A | HIS294 |
| A | HOH533 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG A 454 |
| Chain | Residue |
| A | PRO63 |
| A | LYS66 |
| A | LYS86 |
| A | GLY87 |
| A | HOH597 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE 1PE A 444 |
| Chain | Residue |
| A | THR143 |
| A | LYS166 |
| A | GLU194 |
| A | ASP196 |
| A | LYS221 |
| A | HOH595 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PEG A 555 |
| Chain | Residue |
| A | PHE75 |
| A | ASP76 |
| A | ILE78 |
| A | ASP79 |
| A | LEU80 |
| A | ASP81 |
| A | HOH423 |
| A | HOH470 |
| C | HOH495 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE 1PE A 700 |
| Chain | Residue |
| A | GLU37 |
| A | LEU58 |
| A | LYS61 |
| A | HOH618 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL A 710 |
| Chain | Residue |
| A | GLU207 |
| A | ARG216 |
| A | NAD400 |
| A | PEG802 |
| site_id | BC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 800 |
| Chain | Residue |
| A | LYS53 |
| A | LEU54 |
| A | THR55 |
| A | ASP76 |
| A | HIS77 |
| site_id | BC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE 1PE A 335 |
| Chain | Residue |
| A | GLU99 |
| B | LEU161 |
| B | ALA162 |
| B | 1PE804 |
| site_id | BC5 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE PEG A 701 |
| Chain | Residue |
| A | THR149 |
| A | GLY150 |
| A | ASP171 |
| A | VAL173 |
| A | ARG175 |
| A | NAD400 |
| C | LYS174 |
| C | LYS179 |
| C | 1PE404 |
| C | HOH408 |
| C | PEG702 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PEG A 802 |
| Chain | Residue |
| A | HIS210 |
| A | ASN213 |
| A | ARG216 |
| A | HOH481 |
| A | GOL710 |
| site_id | BC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PEG A 803 |
| Chain | Residue |
| A | GLY164 |
| B | 1PE804 |
| site_id | BC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PEG A 772 |
| Chain | Residue |
| A | VAL123 |
| A | LYS124 |
| A | LEU126 |
| B | LEU281 |
| B | CYS285 |
| C | LEU281 |
| C | CYS285 |
| D | LYS124 |
| D | LEU126 |
| site_id | BC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 711 |
| Chain | Residue |
| A | TYR51 |
| A | ILE264 |
| B | SER129 |
| B | GLN130 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PPI B 398 |
| Chain | Residue |
| B | ARG71 |
| B | TYR297 |
| B | ILE306 |
| B | HOH483 |
| B | HOH522 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE LAC B 399 |
| Chain | Residue |
| B | PHE49 |
| B | SER72 |
| B | VAL73 |
| B | GLY74 |
| B | TYR96 |
| B | ARG231 |
| B | HIS294 |
| B | NAD400 |
| site_id | CC3 |
| Number of Residues | 31 |
| Details | BINDING SITE FOR RESIDUE NAD B 400 |
| Chain | Residue |
| B | VAL73 |
| B | TYR96 |
| B | VAL101 |
| B | GLY150 |
| B | ARG151 |
| B | ILE152 |
| B | TYR170 |
| B | ASP171 |
| B | VAL172 |
| B | HIS201 |
| B | PRO203 |
| B | THR208 |
| B | THR229 |
| B | ALA230 |
| B | ARG231 |
| B | ASP255 |
| B | HIS294 |
| B | ALA296 |
| B | TYR297 |
| B | LAC399 |
| B | HOH401 |
| B | HOH402 |
| B | HOH405 |
| B | HOH408 |
| B | HOH423 |
| B | HOH425 |
| B | HOH448 |
| B | HOH457 |
| B | HOH553 |
| B | HOH603 |
| B | HOH657 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 770 |
| Chain | Residue |
| B | LYS53 |
| B | HIS77 |
| B | ILE78 |
| B | ASP79 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 1PE B 407 |
| Chain | Residue |
| B | SER33 |
| B | GLU37 |
| B | GLU57 |
| B | LEU58 |
| B | LYS61 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE 1PE B 404 |
| Chain | Residue |
| B | TYR170 |
| B | VAL172 |
| B | LYS174 |
| B | LYS179 |
| B | TYR185 |
| site_id | CC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B 777 |
| Chain | Residue |
| B | PHE15 |
| B | ASP222 |
| B | GLY223 |
| B | GLY247 |
| B | HOH585 |
| site_id | CC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 800 |
| Chain | Residue |
| A | LYS124 |
| B | LYS117 |
| B | ASP121 |
| B | ALA284 |
| B | CYS285 |
| D | LYS125 |
| site_id | CC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 801 |
| Chain | Residue |
| A | GLY247 |
| B | GLU207 |
| B | HIS209 |
| B | MSE211 |
| B | ASN213 |
| B | ARG216 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE 1PE B 804 |
| Chain | Residue |
| A | ALA162 |
| A | 1PE335 |
| A | PEG803 |
| B | MSE158 |
| B | TYR159 |
| B | LEU161 |
| B | ALA162 |
| site_id | DC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PEG C 702 |
| Chain | Residue |
| A | VAL172 |
| A | VAL173 |
| A | NAD400 |
| A | PEG701 |
| C | LYS179 |
| C | VAL184 |
| C | TYR185 |
| C | HOH483 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PPI C 398 |
| Chain | Residue |
| C | SER7 |
| C | ARG71 |
| C | TYR297 |
| C | HOH468 |
| D | HOH582 |
| site_id | DC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE LAC C 399 |
| Chain | Residue |
| C | PHE49 |
| C | SER72 |
| C | VAL73 |
| C | GLY74 |
| C | TYR96 |
| C | ARG231 |
| C | HIS294 |
| C | NAD400 |
| site_id | DC5 |
| Number of Residues | 32 |
| Details | BINDING SITE FOR RESIDUE NAD C 400 |
| Chain | Residue |
| C | VAL73 |
| C | TYR96 |
| C | VAL101 |
| C | THR149 |
| C | GLY150 |
| C | ARG151 |
| C | ILE152 |
| C | TYR170 |
| C | ASP171 |
| C | VAL172 |
| C | HIS201 |
| C | PRO203 |
| C | THR208 |
| C | THR229 |
| C | ALA230 |
| C | ARG231 |
| C | ASP255 |
| C | HIS294 |
| C | ALA296 |
| C | TYR297 |
| C | LAC399 |
| C | HOH407 |
| C | HOH410 |
| C | HOH417 |
| C | HOH426 |
| C | HOH451 |
| C | HOH467 |
| C | HOH480 |
| C | HOH487 |
| C | HOH511 |
| C | HOH516 |
| C | HOH533 |
| site_id | DC6 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL C 401 |
| Chain | Residue |
| C | GLU99 |
| D | GLY164 |
| site_id | DC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE 1PE C 404 |
| Chain | Residue |
| A | VAL173 |
| A | LYS174 |
| A | ARG175 |
| A | GLU176 |
| A | HOH498 |
| A | PEG701 |
| C | TYR170 |
| C | ASP171 |
| C | VAL172 |
| C | LYS174 |
| C | THR186 |
| C | SER187 |
| site_id | DC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL C 650 |
| Chain | Residue |
| C | THR55 |
| C | ASP76 |
| C | HIS77 |
| C | ASP79 |
| site_id | DC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PEG C 771 |
| Chain | Residue |
| C | TYR170 |
| C | ARG216 |
| site_id | EC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PPI D 398 |
| Chain | Residue |
| D | ARG71 |
| D | TYR297 |
| D | HOH579 |
| site_id | EC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE LAC D 399 |
| Chain | Residue |
| D | PHE49 |
| D | VAL50 |
| D | SER72 |
| D | VAL73 |
| D | GLY74 |
| D | TYR96 |
| D | ARG231 |
| D | HIS294 |
| D | NAD400 |
| site_id | EC3 |
| Number of Residues | 34 |
| Details | BINDING SITE FOR RESIDUE NAD D 400 |
| Chain | Residue |
| D | VAL73 |
| D | TYR96 |
| D | VAL101 |
| D | GLY150 |
| D | ARG151 |
| D | ILE152 |
| D | TYR170 |
| D | ASP171 |
| D | VAL172 |
| D | HIS201 |
| D | VAL202 |
| D | PRO203 |
| D | THR208 |
| D | THR229 |
| D | ALA230 |
| D | ARG231 |
| D | ASP255 |
| D | HIS294 |
| D | ALA296 |
| D | TYR297 |
| D | LAC399 |
| D | HOH410 |
| D | HOH413 |
| D | HOH420 |
| D | HOH428 |
| D | HOH435 |
| D | HOH438 |
| D | HOH443 |
| D | HOH477 |
| D | HOH486 |
| D | HOH496 |
| D | HOH507 |
| D | HOH529 |
| D | HOH570 |
| site_id | EC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE GOL D 401 |
| Chain | Residue |
| D | ASP222 |
| D | ARG246 |
| site_id | EC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL D 777 |
| Chain | Residue |
| D | LEU54 |
| D | ASP76 |
| D | HIS77 |
| D | ASP79 |
| site_id | EC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PEG D 405 |
| Chain | Residue |
| D | PRO63 |
| D | LEU65 |
| D | LYS86 |
Functional Information from PROSITE/UniProt
| site_id | PS00065 |
| Number of Residues | 28 |
| Details | D_2_HYDROXYACID_DH_1 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. LGVIGtGRIGsrvamyglafgmk.VLcYD |
| Chain | Residue | Details |
| A | LEU144-ASP171 |
| site_id | PS00670 |
| Number of Residues | 23 |
| Details | D_2_HYDROXYACID_DH_2 D-isomer specific 2-hydroxyacid dehydrogenases signature 2. LLkeSDVIsLHvPytkeThhMiN |
| Chain | Residue | Details |
| A | LEU191-ASN213 |
| site_id | PS00671 |
| Number of Residues | 17 |
| Details | D_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. MKdGvYLINtARGkVVD |
| Chain | Residue | Details |
| A | MSE220-ASP236 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1psd |
| Chain | Residue | Details |
| A | HIS294 | |
| A | GLU260 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1psd |
| Chain | Residue | Details |
| B | HIS294 | |
| B | GLU260 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1psd |
| Chain | Residue | Details |
| C | HIS294 | |
| C | GLU260 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1psd |
| Chain | Residue | Details |
| D | HIS294 | |
| D | GLU260 |
