1N7G
Crystal Structure of the GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP-rhamnose.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005525 | molecular_function | GTP binding |
| A | 0005829 | cellular_component | cytosol |
| A | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| A | 0009826 | biological_process | unidimensional cell growth |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019673 | biological_process | GDP-mannose metabolic process |
| A | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
| A | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| B | 0005525 | molecular_function | GTP binding |
| B | 0005829 | cellular_component | cytosol |
| B | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| B | 0009826 | biological_process | unidimensional cell growth |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019673 | biological_process | GDP-mannose metabolic process |
| B | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
| B | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| C | 0005525 | molecular_function | GTP binding |
| C | 0005829 | cellular_component | cytosol |
| C | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| C | 0009826 | biological_process | unidimensional cell growth |
| C | 0016829 | molecular_function | lyase activity |
| C | 0019673 | biological_process | GDP-mannose metabolic process |
| C | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
| C | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| D | 0005525 | molecular_function | GTP binding |
| D | 0005829 | cellular_component | cytosol |
| D | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| D | 0009826 | biological_process | unidimensional cell growth |
| D | 0016829 | molecular_function | lyase activity |
| D | 0019673 | biological_process | GDP-mannose metabolic process |
| D | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
| D | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP A 701 |
| Chain | Residue |
| A | GLY35 |
| A | ALA114 |
| A | ALA115 |
| A | SER117 |
| A | TYR128 |
| A | VAL132 |
| A | ALA160 |
| A | GLY161 |
| A | SER162 |
| A | TYR185 |
| A | LYS189 |
| A | THR37 |
| A | LEU212 |
| A | ASN214 |
| A | HIS215 |
| A | ARG220 |
| A | GDR801 |
| A | HOH806 |
| A | HOH807 |
| A | HOH810 |
| A | HOH820 |
| A | HOH825 |
| A | GLY38 |
| A | HOH837 |
| A | HOH838 |
| A | HOH839 |
| A | HOH847 |
| A | HOH851 |
| A | HOH929 |
| A | HOH931 |
| C | ARG61 |
| C | SER62 |
| C | SER63 |
| A | GLN39 |
| A | ASP40 |
| A | ARG60 |
| A | ASP91 |
| A | LEU92 |
| A | LEU113 |
| site_id | AC2 |
| Number of Residues | 38 |
| Details | BINDING SITE FOR RESIDUE NDP B 702 |
| Chain | Residue |
| A | GDR802 |
| A | HOH862 |
| B | GLY35 |
| B | THR37 |
| B | GLY38 |
| B | GLN39 |
| B | ASP40 |
| B | ARG60 |
| B | ASP91 |
| B | LEU92 |
| B | LEU113 |
| B | ALA114 |
| B | ALA115 |
| B | SER117 |
| B | TYR128 |
| B | VAL132 |
| B | ALA160 |
| B | GLY161 |
| B | SER162 |
| B | TYR185 |
| B | LYS189 |
| B | LEU212 |
| B | ASN214 |
| B | HIS215 |
| B | ARG220 |
| B | HOH705 |
| B | HOH706 |
| B | HOH719 |
| B | HOH721 |
| B | HOH725 |
| B | HOH728 |
| B | HOH733 |
| B | HOH743 |
| B | HOH760 |
| B | HOH778 |
| D | ARG61 |
| D | SER62 |
| D | SER63 |
| site_id | AC3 |
| Number of Residues | 38 |
| Details | BINDING SITE FOR RESIDUE NDP C 703 |
| Chain | Residue |
| C | TYR185 |
| C | LYS189 |
| C | LEU212 |
| C | ASN214 |
| C | HIS215 |
| C | ARG220 |
| C | HOH704 |
| C | HOH719 |
| C | HOH723 |
| C | HOH724 |
| C | HOH726 |
| C | HOH731 |
| C | HOH737 |
| C | HOH747 |
| C | HOH748 |
| C | HOH749 |
| A | ARG61 |
| A | SER62 |
| A | SER63 |
| A | GDR803 |
| A | HOH854 |
| C | GLY35 |
| C | THR37 |
| C | GLY38 |
| C | GLN39 |
| C | ASP40 |
| C | ARG60 |
| C | ASP91 |
| C | LEU92 |
| C | LEU113 |
| C | ALA114 |
| C | ALA115 |
| C | SER117 |
| C | TYR128 |
| C | VAL132 |
| C | ALA160 |
| C | GLY161 |
| C | SER162 |
| site_id | AC4 |
| Number of Residues | 38 |
| Details | BINDING SITE FOR RESIDUE NDP D 704 |
| Chain | Residue |
| B | ARG61 |
| B | SER62 |
| B | SER63 |
| D | GLY35 |
| D | THR37 |
| D | GLY38 |
| D | GLN39 |
| D | ASP40 |
| D | ARG60 |
| D | ASP91 |
| D | LEU92 |
| D | LEU113 |
| D | ALA114 |
| D | ALA115 |
| D | SER117 |
| D | TYR128 |
| D | VAL132 |
| D | ALA160 |
| D | GLY161 |
| D | SER162 |
| D | TYR185 |
| D | LYS189 |
| D | LEU212 |
| D | ASN214 |
| D | HIS215 |
| D | ARG220 |
| D | HOH708 |
| D | HOH709 |
| D | HOH712 |
| D | HOH719 |
| D | HOH720 |
| D | HOH721 |
| D | HOH731 |
| D | HOH769 |
| D | HOH779 |
| D | HOH780 |
| D | HOH795 |
| D | HOH800 |
| site_id | AC5 |
| Number of Residues | 29 |
| Details | BINDING SITE FOR RESIDUE GDR A 801 |
| Chain | Residue |
| A | SER117 |
| A | HIS118 |
| A | VAL119 |
| A | SER162 |
| A | SER163 |
| A | GLU164 |
| A | TYR185 |
| A | ASN214 |
| A | ARG220 |
| A | ASN223 |
| A | PHE224 |
| A | VAL225 |
| A | LYS228 |
| A | GLY247 |
| A | ASN248 |
| A | ALA251 |
| A | ARG253 |
| A | VAL287 |
| A | TYR312 |
| A | ARG314 |
| A | GLU317 |
| A | NDP701 |
| A | HOH822 |
| A | HOH823 |
| A | HOH828 |
| A | HOH832 |
| A | HOH867 |
| A | HOH922 |
| A | HOH931 |
| site_id | AC6 |
| Number of Residues | 29 |
| Details | BINDING SITE FOR RESIDUE GDR A 802 |
| Chain | Residue |
| A | HOH858 |
| A | HOH862 |
| B | SER117 |
| B | HIS118 |
| B | VAL119 |
| B | SER162 |
| B | SER163 |
| B | GLU164 |
| B | TYR185 |
| B | ASN214 |
| B | ARG220 |
| B | ASN223 |
| B | PHE224 |
| B | VAL225 |
| B | LYS228 |
| B | LEU246 |
| B | GLY247 |
| B | ASN248 |
| B | ALA251 |
| B | ARG253 |
| B | VAL287 |
| B | TYR312 |
| B | ARG314 |
| B | GLU317 |
| B | NDP702 |
| B | HOH737 |
| B | HOH748 |
| B | HOH751 |
| B | HOH752 |
| site_id | AC7 |
| Number of Residues | 30 |
| Details | BINDING SITE FOR RESIDUE GDR A 803 |
| Chain | Residue |
| A | HOH854 |
| A | HOH880 |
| A | HOH916 |
| C | SER117 |
| C | HIS118 |
| C | VAL119 |
| C | SER162 |
| C | SER163 |
| C | GLU164 |
| C | TYR185 |
| C | ASN214 |
| C | ARG220 |
| C | ASN223 |
| C | PHE224 |
| C | VAL225 |
| C | LYS228 |
| C | LEU246 |
| C | GLY247 |
| C | ASN248 |
| C | ALA251 |
| C | ARG253 |
| C | VAL287 |
| C | TYR312 |
| C | ARG314 |
| C | GLU317 |
| C | NDP703 |
| C | HOH722 |
| C | HOH735 |
| C | HOH786 |
| C | HOH830 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | ACT_SITE: ACT_SITE => ECO:0000305|PubMed:12501186 |
| Chain | Residue | Details |
| A | SER162 | |
| B | SER162 | |
| C | SER162 | |
| D | SER162 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | ACT_SITE: Nucleophile => ECO:0000305|PubMed:12501186 |
| Chain | Residue | Details |
| A | GLU164 | |
| A | TYR185 | |
| B | GLU164 | |
| B | TYR185 | |
| C | GLU164 | |
| C | TYR185 | |
| D | GLU164 | |
| D | TYR185 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 32 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12501186 |
| Chain | Residue | Details |
| A | GLY35 | |
| B | ARG60 | |
| B | ASP91 | |
| B | LEU113 | |
| B | TYR128 | |
| B | LYS189 | |
| B | HIS215 | |
| B | ARG220 | |
| C | GLY35 | |
| C | ARG60 | |
| C | ASP91 | |
| A | ARG60 | |
| C | LEU113 | |
| C | TYR128 | |
| C | LYS189 | |
| C | HIS215 | |
| C | ARG220 | |
| D | GLY35 | |
| D | ARG60 | |
| D | ASP91 | |
| D | LEU113 | |
| D | TYR128 | |
| A | ASP91 | |
| D | LYS189 | |
| D | HIS215 | |
| D | ARG220 | |
| A | LEU113 | |
| A | TYR128 | |
| A | LYS189 | |
| A | HIS215 | |
| A | ARG220 | |
| B | GLY35 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 28 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:12501186 |
| Chain | Residue | Details |
| A | SER117 | |
| B | TYR185 | |
| B | ASN214 | |
| B | GLY247 | |
| B | ARG253 | |
| B | ARG314 | |
| C | SER117 | |
| C | SER162 | |
| C | TYR185 | |
| C | ASN214 | |
| C | GLY247 | |
| A | SER162 | |
| C | ARG253 | |
| C | ARG314 | |
| D | SER117 | |
| D | SER162 | |
| D | TYR185 | |
| D | ASN214 | |
| D | GLY247 | |
| D | ARG253 | |
| D | ARG314 | |
| A | TYR185 | |
| A | ASN214 | |
| A | GLY247 | |
| A | ARG253 | |
| A | ARG314 | |
| B | SER117 | |
| B | SER162 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR185 | |
| A | LYS189 | |
| A | GLY161 |
| site_id | CSA10 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR185 | |
| B | LYS189 | |
| B | SER162 |
| site_id | CSA11 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | TYR185 | |
| C | LYS189 | |
| C | SER162 |
| site_id | CSA12 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | TYR185 | |
| D | LYS189 | |
| D | SER162 |
| site_id | CSA13 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | ARG182 | |
| A | LYS189 |
| site_id | CSA14 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | ARG182 | |
| B | LYS189 |
| site_id | CSA15 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | ARG182 | |
| C | LYS189 |
| site_id | CSA16 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | ARG182 | |
| D | LYS189 |
| site_id | CSA17 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR185 | |
| A | LYS189 |
| site_id | CSA18 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR185 | |
| B | LYS189 |
| site_id | CSA19 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | TYR185 | |
| C | LYS189 |
| site_id | CSA2 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR185 | |
| B | LYS189 | |
| B | GLY161 |
| site_id | CSA20 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | TYR185 | |
| D | LYS189 |
| site_id | CSA3 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | TYR185 | |
| C | LYS189 | |
| C | GLY161 |
| site_id | CSA4 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | TYR185 | |
| D | LYS189 | |
| D | GLY161 |
| site_id | CSA5 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR185 | |
| A | GLU164 | |
| A | LYS189 | |
| A | SER162 |
| site_id | CSA6 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR185 | |
| B | GLU164 | |
| B | LYS189 | |
| B | SER162 |
| site_id | CSA7 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | TYR185 | |
| C | GLU164 | |
| C | LYS189 | |
| C | SER162 |
| site_id | CSA8 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | TYR185 | |
| D | GLU164 | |
| D | LYS189 | |
| D | SER162 |
| site_id | CSA9 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR185 | |
| A | LYS189 | |
| A | SER162 |
