6DIO
Structure of class II HMG-CoA reductase from Delftia acidovorans with NAD bound
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0004420 | molecular_function | hydroxymethylglutaryl-CoA reductase (NADPH) activity |
| A | 0005778 | cellular_component | peroxisomal membrane |
| A | 0006696 | biological_process | ergosterol biosynthetic process |
| A | 0008299 | biological_process | isoprenoid biosynthetic process |
| A | 0015936 | biological_process | coenzyme A metabolic process |
| 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 | 0140643 | molecular_function | hydroxymethylglutaryl-CoA reductase (NADH) activity |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0004420 | molecular_function | hydroxymethylglutaryl-CoA reductase (NADPH) activity |
| B | 0005778 | cellular_component | peroxisomal membrane |
| B | 0006696 | biological_process | ergosterol biosynthetic process |
| B | 0008299 | biological_process | isoprenoid biosynthetic process |
| B | 0015936 | biological_process | coenzyme A metabolic process |
| 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 | 0140643 | molecular_function | hydroxymethylglutaryl-CoA reductase (NADH) activity |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0004420 | molecular_function | hydroxymethylglutaryl-CoA reductase (NADPH) activity |
| C | 0005778 | cellular_component | peroxisomal membrane |
| C | 0006696 | biological_process | ergosterol biosynthetic process |
| C | 0008299 | biological_process | isoprenoid biosynthetic process |
| C | 0015936 | biological_process | coenzyme A metabolic process |
| 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 | 0140643 | molecular_function | hydroxymethylglutaryl-CoA reductase (NADH) activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 28 |
| Details | binding site for residue NAD A 501 |
| Chain | Residue |
| A | ASP146 |
| A | ALA187 |
| A | ASN188 |
| A | THR189 |
| A | LEU214 |
| A | ASN216 |
| A | ASP283 |
| A | ALA286 |
| A | VAL328 |
| A | GLY329 |
| A | GLY330 |
| A | VAL148 |
| A | EDO507 |
| A | HOH655 |
| B | GLU83 |
| B | THR264 |
| B | LYS267 |
| B | ARG428 |
| B | CIT502 |
| B | EDO512 |
| B | HOH623 |
| A | LEU152 |
| A | VAL181 |
| A | ARG182 |
| A | ASP183 |
| A | ALA184 |
| A | MET185 |
| A | GLY186 |
| site_id | AC2 |
| Number of Residues | 14 |
| Details | binding site for residue CIT A 502 |
| Chain | Residue |
| A | GLU83 |
| A | ARG261 |
| A | THR264 |
| A | LYS267 |
| A | GLY268 |
| A | ASN271 |
| A | ALA368 |
| A | LEU372 |
| A | EDO506 |
| A | HOH643 |
| A | HOH745 |
| A | HOH753 |
| B | ILE213 |
| B | NAD501 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 A 503 |
| Chain | Residue |
| A | HIS125 |
| A | PRO165 |
| A | TYR252 |
| A | EDO511 |
| A | HOH615 |
| A | HOH624 |
| A | HOH681 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 A 504 |
| Chain | Residue |
| A | ARG228 |
| A | THR230 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 505 |
| Chain | Residue |
| A | THR108 |
| A | LEU109 |
| A | ARG135 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 506 |
| Chain | Residue |
| A | SER85 |
| A | ALA89 |
| A | CIT502 |
| A | HOH739 |
| A | HOH753 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 507 |
| Chain | Residue |
| A | ASN191 |
| A | GLU195 |
| A | ARG212 |
| A | ILE213 |
| A | NAD501 |
| A | HOH771 |
| B | LEU372 |
| B | CIT502 |
| site_id | AC8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 508 |
| Chain | Residue |
| A | ARG128 |
| A | ARG306 |
| A | SER318 |
| A | GLU320 |
| A | HOH727 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO A 509 |
| Chain | Residue |
| A | ARG145 |
| A | ASP146 |
| A | THR189 |
| A | THR192 |
| A | MET193 |
| A | HOH620 |
| A | HOH642 |
| A | HOH795 |
| site_id | AD1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 510 |
| Chain | Residue |
| A | VAL209 |
| A | ARG210 |
| A | ARG212 |
| B | ARG239 |
| B | ALA373 |
| B | GLU375 |
| site_id | AD2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 511 |
| Chain | Residue |
| A | TYR252 |
| A | THR253 |
| A | TRP307 |
| A | SO4503 |
| B | ARG169 |
| site_id | AD3 |
| Number of Residues | 21 |
| Details | binding site for residue NAD B 501 |
| Chain | Residue |
| B | ASP183 |
| B | ALA184 |
| B | MET185 |
| B | GLY186 |
| B | ALA187 |
| B | ASN188 |
| B | THR189 |
| B | LEU214 |
| B | ASN216 |
| B | ASP283 |
| B | GLY329 |
| B | HOH703 |
| B | HOH779 |
| A | GLU83 |
| A | LYS267 |
| A | CIT502 |
| A | HOH658 |
| B | ASP146 |
| B | LEU152 |
| B | VAL181 |
| B | ARG182 |
| site_id | AD4 |
| Number of Residues | 15 |
| Details | binding site for residue CIT B 502 |
| Chain | Residue |
| A | ILE213 |
| A | NAD501 |
| A | EDO507 |
| B | GLU83 |
| B | ARG261 |
| B | THR264 |
| B | LYS267 |
| B | GLY268 |
| B | ASN271 |
| B | ALA368 |
| B | LEU372 |
| B | HOH645 |
| B | HOH649 |
| B | HOH680 |
| B | HOH733 |
| site_id | AD5 |
| Number of Residues | 4 |
| Details | binding site for residue SO4 B 503 |
| Chain | Residue |
| B | ASN9 |
| B | ARG11 |
| B | EDO516 |
| B | HOH700 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue SO4 B 504 |
| Chain | Residue |
| B | TYR252 |
| B | HOH704 |
| B | HOH740 |
| B | HOH746 |
| C | HIS125 |
| C | PRO165 |
| site_id | AD7 |
| Number of Residues | 7 |
| Details | binding site for residue SO4 B 505 |
| Chain | Residue |
| B | HIS125 |
| B | PRO165 |
| B | HOH612 |
| B | HOH635 |
| B | HOH751 |
| C | TYR252 |
| C | HOH736 |
| site_id | AD8 |
| Number of Residues | 2 |
| Details | binding site for residue SO4 B 506 |
| Chain | Residue |
| B | HIS385 |
| B | ASN388 |
| site_id | AD9 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 507 |
| Chain | Residue |
| B | ARG228 |
| B | THR230 |
| B | HOH782 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 B 508 |
| Chain | Residue |
| B | ILE389 |
| B | ARG414 |
| B | THR415 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 509 |
| Chain | Residue |
| B | THR108 |
| B | LEU109 |
| C | ARG135 |
| C | HOH627 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 510 |
| Chain | Residue |
| B | ILE204 |
| B | HOH657 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 511 |
| Chain | Residue |
| B | ARG306 |
| B | SER318 |
| B | GLU320 |
| B | EDO518 |
| C | ARG128 |
| C | HOH691 |
| site_id | AE5 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 512 |
| Chain | Residue |
| A | GLY330 |
| A | NAD501 |
| B | PRO84 |
| B | ARG428 |
| B | HOH610 |
| B | HOH673 |
| B | HOH735 |
| site_id | AE6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 513 |
| Chain | Residue |
| B | GLY380 |
| B | MET382 |
| B | ALA383 |
| site_id | AE7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 514 |
| Chain | Residue |
| B | ARG128 |
| B | VAL161 |
| B | HIS162 |
| B | VAL163 |
| B | EDO519 |
| site_id | AE8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 515 |
| Chain | Residue |
| B | GLY397 |
| B | ASP398 |
| C | HOH685 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 516 |
| Chain | Residue |
| B | ARG11 |
| B | ASN67 |
| B | TYR92 |
| B | SO4503 |
| B | HOH607 |
| site_id | AF1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 517 |
| Chain | Residue |
| A | GLY299 |
| A | SER300 |
| B | SER296 |
| B | ARG297 |
| B | GLY299 |
| B | HOH634 |
| site_id | AF2 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 518 |
| Chain | Residue |
| B | ARG306 |
| B | EDO511 |
| C | VAL163 |
| C | EDO512 |
| C | HOH605 |
| C | HOH808 |
| site_id | AF3 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 519 |
| Chain | Residue |
| B | HIS125 |
| B | EDO514 |
| B | HOH614 |
| B | HOH658 |
| C | ARG306 |
| C | EDO514 |
| C | HOH611 |
| site_id | AF4 |
| Number of Residues | 26 |
| Details | binding site for residue NAD C 501 |
| Chain | Residue |
| C | GLU83 |
| C | ASP146 |
| C | VAL148 |
| C | LEU152 |
| C | VAL181 |
| C | ARG182 |
| C | ASP183 |
| C | ALA184 |
| C | MET185 |
| C | GLY186 |
| C | ALA187 |
| C | ASN188 |
| C | THR189 |
| C | ASN191 |
| C | LEU214 |
| C | ASN216 |
| C | LYS267 |
| C | ASP283 |
| C | VAL328 |
| C | GLY329 |
| C | GLY330 |
| C | ARG428 |
| C | CIT502 |
| C | HOH630 |
| C | HOH686 |
| C | HOH730 |
| site_id | AF5 |
| Number of Residues | 13 |
| Details | binding site for residue CIT C 502 |
| Chain | Residue |
| C | GLU83 |
| C | ARG261 |
| C | THR264 |
| C | LYS267 |
| C | GLY268 |
| C | ASN271 |
| C | ALA368 |
| C | LEU372 |
| C | NAD501 |
| C | HOH677 |
| C | HOH742 |
| C | HOH748 |
| C | HOH755 |
| site_id | AF6 |
| Number of Residues | 1 |
| Details | binding site for residue SO4 C 503 |
| Chain | Residue |
| C | ARG228 |
| site_id | AF7 |
| Number of Residues | 3 |
| Details | binding site for residue SO4 C 504 |
| Chain | Residue |
| C | ARG239 |
| C | ILE377 |
| C | GLN378 |
| site_id | AF8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 505 |
| Chain | Residue |
| B | ARG135 |
| C | THR108 |
| C | LEU109 |
| C | HOH616 |
| site_id | AF9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 506 |
| Chain | Residue |
| C | LEU7 |
| C | ASN9 |
| C | PHE10 |
| C | ARG11 |
| C | EDO509 |
| C | HOH775 |
| C | HOH832 |
| site_id | AG1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 507 |
| Chain | Residue |
| C | GLN137 |
| C | GLU140 |
| C | ARG141 |
| site_id | AG2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 508 |
| Chain | Residue |
| C | MET50 |
| C | GLY330 |
| C | LEU425 |
| C | HOH609 |
| C | HOH753 |
| site_id | AG3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 509 |
| Chain | Residue |
| C | ASN67 |
| C | LYS95 |
| C | EDO506 |
| C | HOH654 |
| C | HOH801 |
| site_id | AG4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 510 |
| Chain | Residue |
| C | ARG339 |
| C | HOH767 |
| site_id | AG5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 511 |
| Chain | Residue |
| C | HIS385 |
| C | ASN388 |
| C | HOH812 |
| site_id | AG6 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 512 |
| Chain | Residue |
| B | ARG297 |
| B | EDO518 |
| C | HIS162 |
| site_id | AG7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO C 513 |
| Chain | Residue |
| C | GLY376 |
| C | GLY380 |
| C | ALA383 |
| site_id | AG8 |
| Number of Residues | 8 |
| Details | binding site for residue EDO C 514 |
| Chain | Residue |
| B | HIS125 |
| B | ARG128 |
| B | EDO519 |
| C | ARG306 |
| C | SER318 |
| C | GLU320 |
| C | HOH611 |
| C | HOH689 |
Functional Information from PROSITE/UniProt
| site_id | PS00066 |
| Number of Residues | 15 |
| Details | HMG_COA_REDUCTASE_1 Hydroxymethylglutaryl-coenzyme A reductases signature 1. HlIVdVRDaMGaNtV |
| Chain | Residue | Details |
| A | HIS176-VAL190 |
| site_id | PS00318 |
| Number of Residues | 8 |
| Details | HMG_COA_REDUCTASE_2 Hydroxymethylglutaryl-coenzyme A reductases signature 2. VGlVGGAT |
| Chain | Residue | Details |
| A | VAL325-THR332 |
| site_id | PS01192 |
| Number of Residues | 14 |
| Details | HMG_COA_REDUCTASE_3 Hydroxymethylglutaryl-coenzyme A reductases signature 3. ALaTegIqRGHMaL |
| Chain | Residue | Details |
| A | ALA371-LEU384 |
