5V7N
Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with NADP and 2-Keto-D-gluconic acid
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000166 | molecular_function | nucleotide binding |
| A | 0005829 | cellular_component | cytosol |
| 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 | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| A | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0051287 | molecular_function | NAD binding |
| B | 0000166 | molecular_function | nucleotide binding |
| B | 0005829 | cellular_component | cytosol |
| 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 | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| B | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0051287 | molecular_function | NAD binding |
| C | 0000166 | molecular_function | nucleotide binding |
| C | 0005829 | cellular_component | cytosol |
| 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 | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| C | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0051287 | molecular_function | NAD binding |
| D | 0000166 | molecular_function | nucleotide binding |
| D | 0005829 | cellular_component | cytosol |
| 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 | 0016618 | molecular_function | hydroxypyruvate reductase [NAD(P)H] activity |
| D | 0030267 | molecular_function | glyoxylate reductase (NADPH) activity |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0051287 | molecular_function | NAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 38 |
| Details | binding site for residue NAP A 401 |
| Chain | Residue |
| A | VAL72 |
| A | THR174 |
| A | ILE200 |
| A | VAL201 |
| A | PRO202 |
| A | SER206 |
| A | THR207 |
| A | VAL228 |
| A | GLY229 |
| A | ARG230 |
| A | ASP254 |
| A | VAL100 |
| A | HIS277 |
| A | ALA279 |
| A | 8YV402 |
| A | MG408 |
| A | HOH508 |
| A | HOH545 |
| A | HOH555 |
| A | HOH576 |
| A | HOH583 |
| A | HOH608 |
| A | PHE148 |
| A | HOH610 |
| A | HOH621 |
| A | HOH624 |
| A | HOH634 |
| A | HOH642 |
| A | HOH655 |
| A | HOH659 |
| A | HOH696 |
| A | HOH724 |
| A | LEU150 |
| A | GLY151 |
| A | ARG152 |
| A | ILE153 |
| A | THR172 |
| A | ARG173 |
| site_id | AC2 |
| Number of Residues | 16 |
| Details | binding site for residue 8YV A 402 |
| Chain | Residue |
| A | SER50 |
| A | GLY51 |
| A | PHE70 |
| A | GLY71 |
| A | VAL72 |
| A | GLY73 |
| A | LEU96 |
| A | ARG230 |
| A | HIS277 |
| A | SER280 |
| A | ARG286 |
| A | MET289 |
| A | NAP401 |
| A | HOH515 |
| A | HOH598 |
| A | HOH690 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue NA A 403 |
| Chain | Residue |
| A | ALA191 |
| A | GLU192 |
| A | VAL194 |
| A | ALA218 |
| A | LEU219 |
| A | HOH626 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue PEG A 404 |
| Chain | Residue |
| A | ARG28 |
| A | GLU30 |
| A | PRO137 |
| A | PG4407 |
| A | HOH732 |
| B | VAL283 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue CL A 405 |
| Chain | Residue |
| A | ASN13 |
| A | ARG286 |
| A | HOH779 |
| site_id | AC6 |
| Number of Residues | 1 |
| Details | binding site for residue CL A 406 |
| Chain | Residue |
| A | ALA34 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue PG4 A 407 |
| Chain | Residue |
| A | LYS11 |
| A | GLU30 |
| A | PRO134 |
| A | PRO137 |
| A | PEG404 |
| A | HOH582 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 408 |
| Chain | Residue |
| A | NAP401 |
| A | HOH724 |
| A | HOH738 |
| A | HOH746 |
| A | HOH763 |
| A | HOH812 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue MG A 409 |
| Chain | Residue |
| A | HOH527 |
| A | HOH595 |
| A | HOH800 |
| A | HOH802 |
| A | HOH830 |
| A | HOH860 |
| site_id | AD1 |
| Number of Residues | 38 |
| Details | binding site for residue NAP B 401 |
| Chain | Residue |
| B | VAL201 |
| B | PRO202 |
| B | SER206 |
| B | THR207 |
| B | VAL228 |
| B | GLY229 |
| B | ARG230 |
| B | ASP254 |
| B | HIS277 |
| B | ALA279 |
| B | 8YV402 |
| B | MG408 |
| B | HOH518 |
| B | HOH522 |
| B | HOH525 |
| B | HOH538 |
| B | HOH560 |
| B | HOH584 |
| B | HOH601 |
| B | HOH604 |
| B | HOH605 |
| B | HOH616 |
| B | HOH623 |
| B | HOH660 |
| B | HOH682 |
| B | HOH710 |
| B | HOH723 |
| B | VAL72 |
| B | VAL100 |
| B | PHE148 |
| B | LEU150 |
| B | GLY151 |
| B | ARG152 |
| B | ILE153 |
| B | THR172 |
| B | ARG173 |
| B | THR174 |
| B | ILE200 |
| site_id | AD2 |
| Number of Residues | 16 |
| Details | binding site for residue 8YV B 402 |
| Chain | Residue |
| B | SER50 |
| B | GLY51 |
| B | PHE70 |
| B | GLY71 |
| B | VAL72 |
| B | GLY73 |
| B | LEU96 |
| B | ARG230 |
| B | HIS277 |
| B | SER280 |
| B | ARG286 |
| B | MET289 |
| B | NAP401 |
| B | HOH528 |
| B | HOH598 |
| B | HOH658 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue NA B 403 |
| Chain | Residue |
| B | ALA191 |
| B | GLU192 |
| B | VAL194 |
| B | ALA218 |
| B | LEU219 |
| B | HOH724 |
| site_id | AD4 |
| Number of Residues | 4 |
| Details | binding site for residue CL B 404 |
| Chain | Residue |
| B | ASN13 |
| B | ARG286 |
| B | HOH763 |
| B | HOH773 |
| site_id | AD5 |
| Number of Residues | 1 |
| Details | binding site for residue CL B 405 |
| Chain | Residue |
| B | ALA34 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue GOL B 406 |
| Chain | Residue |
| B | VAL95 |
| B | THR285 |
| B | ALA288 |
| B | HOH504 |
| B | HOH526 |
| B | HOH665 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 407 |
| Chain | Residue |
| A | HOH702 |
| A | HOH717 |
| A | HOH744 |
| B | ALA319 |
| B | HOH681 |
| B | HOH725 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue MG B 408 |
| Chain | Residue |
| B | NAP401 |
| B | HOH616 |
| B | HOH710 |
| B | HOH723 |
| B | HOH739 |
| B | HOH808 |
| site_id | AD9 |
| Number of Residues | 41 |
| Details | binding site for residue NAP C 401 |
| Chain | Residue |
| C | VAL72 |
| C | VAL100 |
| C | PHE148 |
| C | GLY149 |
| C | LEU150 |
| C | GLY151 |
| C | ARG152 |
| C | ILE153 |
| C | THR172 |
| C | ARG173 |
| C | THR174 |
| C | ILE200 |
| C | VAL201 |
| C | PRO202 |
| C | SER206 |
| C | THR207 |
| C | VAL228 |
| C | GLY229 |
| C | ARG230 |
| C | ASP254 |
| C | HIS277 |
| C | ALA279 |
| C | 8YV402 |
| C | MG405 |
| C | HOH505 |
| C | HOH506 |
| C | HOH511 |
| C | HOH512 |
| C | HOH529 |
| C | HOH533 |
| C | HOH547 |
| C | HOH550 |
| C | HOH558 |
| C | HOH565 |
| C | HOH598 |
| C | HOH617 |
| C | HOH618 |
| C | HOH626 |
| C | HOH628 |
| C | HOH629 |
| C | HOH654 |
| site_id | AE1 |
| Number of Residues | 16 |
| Details | binding site for residue 8YV C 402 |
| Chain | Residue |
| C | GLY51 |
| C | PHE70 |
| C | GLY71 |
| C | VAL72 |
| C | GLY73 |
| C | LEU96 |
| C | ARG230 |
| C | HIS277 |
| C | SER280 |
| C | ARG286 |
| C | MET289 |
| C | NAP401 |
| C | HOH514 |
| C | HOH548 |
| C | HOH602 |
| C | HOH624 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue NA C 403 |
| Chain | Residue |
| C | ALA191 |
| C | GLU192 |
| C | VAL194 |
| C | ALA218 |
| C | LEU219 |
| C | HOH643 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue CL C 404 |
| Chain | Residue |
| C | ASN13 |
| C | ARG286 |
| site_id | AE4 |
| Number of Residues | 6 |
| Details | binding site for residue MG C 405 |
| Chain | Residue |
| C | NAP401 |
| C | HOH533 |
| C | HOH618 |
| C | HOH628 |
| C | HOH716 |
| C | HOH770 |
| site_id | AE5 |
| Number of Residues | 40 |
| Details | binding site for residue NAP D 401 |
| Chain | Residue |
| D | VAL72 |
| D | VAL100 |
| D | PHE148 |
| D | LEU150 |
| D | GLY151 |
| D | ARG152 |
| D | ILE153 |
| D | THR172 |
| D | ARG173 |
| D | THR174 |
| D | ILE200 |
| D | VAL201 |
| D | PRO202 |
| D | SER206 |
| D | THR207 |
| D | VAL228 |
| D | GLY229 |
| D | ARG230 |
| D | ASP254 |
| D | HIS277 |
| D | ALA279 |
| D | 8YV402 |
| D | MG408 |
| D | HOH519 |
| D | HOH533 |
| D | HOH535 |
| D | HOH536 |
| D | HOH537 |
| D | HOH550 |
| D | HOH557 |
| D | HOH562 |
| D | HOH566 |
| D | HOH577 |
| D | HOH591 |
| D | HOH620 |
| D | HOH629 |
| D | HOH636 |
| D | HOH651 |
| D | HOH676 |
| D | HOH684 |
| site_id | AE6 |
| Number of Residues | 16 |
| Details | binding site for residue 8YV D 402 |
| Chain | Residue |
| D | SER50 |
| D | GLY51 |
| D | PHE70 |
| D | GLY71 |
| D | VAL72 |
| D | GLY73 |
| D | LEU96 |
| D | ARG230 |
| D | HIS277 |
| D | SER280 |
| D | ARG286 |
| D | MET289 |
| D | NAP401 |
| D | HOH565 |
| D | HOH609 |
| D | HOH657 |
| site_id | AE7 |
| Number of Residues | 6 |
| Details | binding site for residue NA D 403 |
| Chain | Residue |
| D | ALA191 |
| D | GLU192 |
| D | VAL194 |
| D | ALA218 |
| D | LEU219 |
| D | HOH705 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue PEG D 404 |
| Chain | Residue |
| C | VAL283 |
| D | GLU30 |
| D | PRO137 |
| D | LYS222 |
| D | HOH679 |
| site_id | AE9 |
| Number of Residues | 4 |
| Details | binding site for residue CL D 405 |
| Chain | Residue |
| D | ASN13 |
| D | ARG286 |
| D | HOH707 |
| D | HOH724 |
| site_id | AF1 |
| Number of Residues | 1 |
| Details | binding site for residue CL D 406 |
| Chain | Residue |
| D | ALA34 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue GOL D 407 |
| Chain | Residue |
| D | VAL95 |
| D | THR285 |
| D | ALA288 |
| D | HOH517 |
| site_id | AF3 |
| Number of Residues | 6 |
| Details | binding site for residue MG D 408 |
| Chain | Residue |
| D | NAP401 |
| D | HOH519 |
| D | HOH620 |
| D | HOH684 |
| D | HOH692 |
| D | HOH770 |
| site_id | AF4 |
| Number of Residues | 5 |
| Details | binding site for residue MG D 409 |
| Chain | Residue |
| D | HOH597 |
| D | HOH633 |
| D | HOH761 |
| D | HOH771 |
| D | HOH804 |
