4RGQ
Crystal structure of the Methanocaldococcus jannaschii G1PDH with NADPH and DHAP
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0006650 | biological_process | glycerophospholipid metabolic process |
| A | 0008654 | biological_process | phospholipid biosynthetic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050492 | molecular_function | glycerol-1-phosphate dehydrogenase [NAD(P)+] activity |
| A | 0106357 | molecular_function | glycerol-1-phosphate dehydrogenase (NAD+) activity |
| A | 0106358 | molecular_function | glycerol-1-phosphate dehydrogenase (NADP+) activity |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0006650 | biological_process | glycerophospholipid metabolic process |
| B | 0008654 | biological_process | phospholipid biosynthetic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050492 | molecular_function | glycerol-1-phosphate dehydrogenase [NAD(P)+] activity |
| B | 0106357 | molecular_function | glycerol-1-phosphate dehydrogenase (NAD+) activity |
| B | 0106358 | molecular_function | glycerol-1-phosphate dehydrogenase (NADP+) activity |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0006650 | biological_process | glycerophospholipid metabolic process |
| C | 0008654 | biological_process | phospholipid biosynthetic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0050492 | molecular_function | glycerol-1-phosphate dehydrogenase [NAD(P)+] activity |
| C | 0106357 | molecular_function | glycerol-1-phosphate dehydrogenase (NAD+) activity |
| C | 0106358 | molecular_function | glycerol-1-phosphate dehydrogenase (NADP+) activity |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0006650 | biological_process | glycerophospholipid metabolic process |
| D | 0008654 | biological_process | phospholipid biosynthetic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016614 | molecular_function | oxidoreductase activity, acting on CH-OH group of donors |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0050492 | molecular_function | glycerol-1-phosphate dehydrogenase [NAD(P)+] activity |
| D | 0106357 | molecular_function | glycerol-1-phosphate dehydrogenase (NAD+) activity |
| D | 0106358 | molecular_function | glycerol-1-phosphate dehydrogenase (NADP+) activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE NDP A 401 |
| Chain | Residue |
| A | GLY36 |
| A | THR101 |
| A | SER103 |
| A | ASN104 |
| A | GLY106 |
| A | SER109 |
| A | ILE111 |
| A | SER113 |
| A | SER137 |
| A | PRO138 |
| A | LEU141 |
| A | LYS37 |
| A | HIS247 |
| A | 13P404 |
| A | HOH510 |
| A | HOH520 |
| A | HOH529 |
| A | HOH536 |
| A | HOH570 |
| A | HOH635 |
| A | HOH637 |
| A | ASN38 |
| A | THR39 |
| A | TYR52 |
| A | GLY78 |
| A | ARG79 |
| A | ASP82 |
| A | THR100 |
| site_id | AC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K A 402 |
| Chain | Residue |
| A | ASP105 |
| A | ASP148 |
| A | ASN152 |
| A | ALA221 |
| A | 13P404 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN A 403 |
| Chain | Residue |
| A | ASP105 |
| A | ASP148 |
| A | HIS226 |
| A | HIS247 |
| A | 13P404 |
| site_id | AC4 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 13P A 404 |
| Chain | Residue |
| A | ASP105 |
| A | GLN116 |
| A | SER118 |
| A | SER218 |
| A | ALA221 |
| A | SER222 |
| A | HIS226 |
| A | HIS230 |
| A | HIS247 |
| A | ARG310 |
| A | NDP401 |
| A | K402 |
| A | ZN403 |
| A | HOH543 |
| A | HOH637 |
| site_id | AC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO A 405 |
| Chain | Residue |
| A | ILE3 |
| A | VAL4 |
| A | PRO110 |
| A | VAL121 |
| A | ALA123 |
| A | ALA213 |
| A | ASN216 |
| site_id | AC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE EDO A 406 |
| Chain | Residue |
| A | LYS85 |
| A | ALA88 |
| A | TYR89 |
| A | PHE95 |
| A | VAL121 |
| A | ASP122 |
| A | ALA123 |
| A | PRO124 |
| A | HOH502 |
| A | HOH579 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO A 407 |
| Chain | Residue |
| A | ASN17 |
| A | ILE19 |
| A | GLU20 |
| A | TYR47 |
| A | HOH508 |
| A | HOH530 |
| A | HOH611 |
| B | SER270 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 408 |
| Chain | Residue |
| A | ARG139 |
| A | SER143 |
| A | HOH617 |
| site_id | AC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 409 |
| Chain | Residue |
| A | LYS90 |
| A | LEU91 |
| A | GLY92 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO A 410 |
| Chain | Residue |
| A | PRO138 |
| C | GLU274 |
| site_id | BC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO A 411 |
| Chain | Residue |
| A | TYR260 |
| A | LYS264 |
| A | GLU324 |
| A | GLU331 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 412 |
| Chain | Residue |
| A | ILE2 |
| A | ILE3 |
| B | ILE11 |
| site_id | BC4 |
| Number of Residues | 26 |
| Details | BINDING SITE FOR RESIDUE NDP B 401 |
| Chain | Residue |
| B | GLY77 |
| B | GLY78 |
| B | ARG79 |
| B | ASP82 |
| B | THR100 |
| B | THR101 |
| B | SER103 |
| B | ASN104 |
| B | GLY106 |
| B | SER109 |
| B | ILE111 |
| B | SER113 |
| B | SER137 |
| B | LEU141 |
| B | HIS247 |
| B | 1GP404 |
| B | HOH506 |
| B | HOH518 |
| B | HOH533 |
| B | HOH547 |
| B | GLY36 |
| B | LYS37 |
| B | ASN38 |
| B | THR39 |
| B | TYR42 |
| B | TYR52 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K B 402 |
| Chain | Residue |
| B | ASP105 |
| B | ASP148 |
| B | ASN152 |
| B | ALA221 |
| B | 1GP404 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN B 403 |
| Chain | Residue |
| B | ASP105 |
| B | ASP148 |
| B | HIS226 |
| B | HIS247 |
| B | 1GP404 |
| site_id | BC7 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE 1GP B 404 |
| Chain | Residue |
| B | ASP105 |
| B | SER113 |
| B | GLN116 |
| B | SER118 |
| B | ASP148 |
| B | SER218 |
| B | ALA221 |
| B | SER222 |
| B | HIS226 |
| B | HIS230 |
| B | ARG310 |
| B | NDP401 |
| B | K402 |
| B | ZN403 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO B 405 |
| Chain | Residue |
| B | CYS43 |
| B | ARG44 |
| B | PHE45 |
| B | HOH606 |
| D | LYS282 |
| D | VAL283 |
| D | ASP284 |
| site_id | BC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE EDO B 406 |
| Chain | Residue |
| B | ILE3 |
| B | VAL4 |
| B | PRO110 |
| B | MET120 |
| B | VAL121 |
| B | ALA123 |
| B | ALA213 |
| B | ASN216 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 407 |
| Chain | Residue |
| B | LYS264 |
| B | GLU324 |
| B | GLU331 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO B 408 |
| Chain | Residue |
| B | LEU26 |
| B | HOH604 |
| B | HOH618 |
| site_id | CC3 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE NDP C 401 |
| Chain | Residue |
| C | GLY36 |
| C | LYS37 |
| C | ASN38 |
| C | THR39 |
| C | TYR42 |
| C | TYR52 |
| C | GLY77 |
| C | GLY78 |
| C | ARG79 |
| C | ASP82 |
| C | THR100 |
| C | THR101 |
| C | SER103 |
| C | ASN104 |
| C | GLY106 |
| C | ILE111 |
| C | SER113 |
| C | SER137 |
| C | LEU141 |
| C | HIS247 |
| C | 13P404 |
| C | HOH537 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K C 402 |
| Chain | Residue |
| C | ASP105 |
| C | ASP148 |
| C | ASN152 |
| C | ALA221 |
| C | 13P404 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE ZN C 403 |
| Chain | Residue |
| C | ASP148 |
| C | HIS226 |
| C | HIS247 |
| C | 13P404 |
| C | HOH501 |
| site_id | CC6 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE 13P C 404 |
| Chain | Residue |
| C | ASP105 |
| C | SER118 |
| C | ASP148 |
| C | SER218 |
| C | ALA221 |
| C | SER222 |
| C | HIS226 |
| C | HIS230 |
| C | HIS247 |
| C | ARG310 |
| C | NDP401 |
| C | K402 |
| C | ZN403 |
| C | HOH501 |
| C | HOH527 |
| C | HOH580 |
| site_id | CC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO C 405 |
| Chain | Residue |
| C | SER143 |
| C | VAL283 |
| site_id | CC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO C 406 |
| Chain | Residue |
| C | GLU168 |
| C | SER217 |
| site_id | CC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO C 407 |
| Chain | Residue |
| C | ILE2 |
| D | ILE10 |
| D | ILE11 |
| D | HOH597 |
| site_id | DC1 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE NDP D 401 |
| Chain | Residue |
| D | GLY36 |
| D | LYS37 |
| D | ASN38 |
| D | THR39 |
| D | TYR52 |
| D | GLY77 |
| D | GLY78 |
| D | ARG79 |
| D | ASP82 |
| D | THR100 |
| D | THR101 |
| D | SER103 |
| D | ASN104 |
| D | GLY106 |
| D | SER109 |
| D | ILE111 |
| D | SER113 |
| D | SER137 |
| D | PRO138 |
| D | LEU141 |
| D | HIS247 |
| D | 13P404 |
| D | HOH501 |
| D | HOH516 |
| D | HOH520 |
| D | HOH540 |
| D | HOH543 |
| D | HOH560 |
| site_id | DC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE K D 402 |
| Chain | Residue |
| D | ASP105 |
| D | ASP148 |
| D | ASN152 |
| D | ALA221 |
| D | 13P404 |
| site_id | DC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE ZN D 403 |
| Chain | Residue |
| D | ASP105 |
| D | ASP148 |
| D | HIS226 |
| D | HIS247 |
| D | 13P404 |
| D | HOH501 |
| site_id | DC4 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE 13P D 404 |
| Chain | Residue |
| D | ASP105 |
| D | SER113 |
| D | SER118 |
| D | SER218 |
| D | ALA221 |
| D | SER222 |
| D | HIS226 |
| D | HIS230 |
| D | HIS247 |
| D | ARG310 |
| D | NDP401 |
| D | K402 |
| D | ZN403 |
| D | HOH501 |
| D | HOH525 |
| site_id | DC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE EDO D 405 |
| Chain | Residue |
| B | LYS282 |
| B | VAL283 |
| B | ASP284 |
| D | CYS43 |
| D | ARG44 |
| D | PHE45 |
| site_id | DC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO D 406 |
| Chain | Residue |
| D | ILE3 |
| D | VAL4 |
| D | PRO110 |
| D | VAL121 |
| D | ALA123 |
| D | ALA213 |
| D | ASN216 |
| site_id | DC7 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO D 407 |
| Chain | Residue |
| D | LYS179 |
| D | HOH594 |
| site_id | DC8 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO D 408 |
| Chain | Residue |
| D | LYS203 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 32 |
| Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_00497 |
| Chain | Residue | Details |
| A | GLY78 | |
| B | THR100 | |
| B | ASP105 | |
| B | SER109 | |
| B | ASP148 | |
| B | HIS226 | |
| B | HIS230 | |
| B | HIS247 | |
| C | GLY78 | |
| C | THR100 | |
| C | ASP105 | |
| A | THR100 | |
| C | SER109 | |
| C | ASP148 | |
| C | HIS226 | |
| C | HIS230 | |
| C | HIS247 | |
| D | GLY78 | |
| D | THR100 | |
| D | ASP105 | |
| D | SER109 | |
| D | ASP148 | |
| A | ASP105 | |
| D | HIS226 | |
| D | HIS230 | |
| D | HIS247 | |
| A | SER109 | |
| A | ASP148 | |
| A | HIS226 | |
| A | HIS230 | |
| A | HIS247 | |
| B | GLY78 |
