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 | 0008720 | molecular_function | D-lactate dehydrogenase activity |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
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 | 0008720 | molecular_function | D-lactate dehydrogenase activity |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
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 | 0008720 | molecular_function | D-lactate dehydrogenase activity |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
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 | 0008720 | molecular_function | D-lactate dehydrogenase activity |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
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 |