1N7H
Crystal Structure of GDP-mannose 4,6-dehydratase ternary complex with NADPH and GDP
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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP A 601 |
| 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 | HOH604 |
| A | HOH609 |
| A | HOH611 |
| A | HOH612 |
| A | HOH615 |
| A | HOH617 |
| A | GLY38 |
| A | HOH620 |
| A | HOH624 |
| A | HOH637 |
| A | HOH639 |
| A | HOH640 |
| A | HOH643 |
| B | ARG61 |
| B | SER62 |
| B | SER63 |
| B | HOH840 |
| A | GLN39 |
| A | ASP40 |
| A | ARG60 |
| A | ASP91 |
| A | LEU92 |
| A | LEU113 |
| site_id | AC2 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE GDP A 602 |
| Chain | Residue |
| A | HIS118 |
| A | VAL119 |
| A | GLU164 |
| A | ASN214 |
| A | ASN223 |
| A | PHE224 |
| A | VAL225 |
| A | LYS228 |
| A | LEU246 |
| A | GLY247 |
| A | ASN248 |
| A | ALA251 |
| A | ARG253 |
| A | VAL287 |
| A | TYR312 |
| A | ARG314 |
| A | GLU317 |
| A | HOH621 |
| A | HOH623 |
| A | HOH632 |
| A | HOH636 |
| A | HOH641 |
| A | HOH673 |
| A | HOH738 |
| A | HOH803 |
| site_id | AC3 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP B 701 |
| Chain | Residue |
| B | HOH726 |
| B | HOH740 |
| B | HOH783 |
| B | HOH811 |
| A | ARG61 |
| A | SER62 |
| A | SER63 |
| A | HOH635 |
| A | HOH651 |
| 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 | HOH706 |
| B | HOH708 |
| B | HOH710 |
| B | HOH714 |
| B | HOH721 |
| B | HOH722 |
| B | HOH724 |
| site_id | AC4 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE GDP B 702 |
| Chain | Residue |
| B | VAL119 |
| B | GLU164 |
| B | ASN214 |
| 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 | HOH720 |
| B | HOH723 |
| B | HOH730 |
| B | HOH753 |
| B | HOH770 |
| B | HOH780 |
| B | HOH812 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 2 |
| Details | ACT_SITE: ACT_SITE => ECO:0000305|PubMed:12501186 |
| Chain | Residue | Details |
| A | SER162 | |
| B | SER162 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 4 |
| Details | ACT_SITE: Nucleophile => ECO:0000305|PubMed:12501186 |
| Chain | Residue | Details |
| A | GLU164 | |
| A | TYR185 | |
| B | GLU164 | |
| B | TYR185 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| 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 | |
| A | ARG60 | |
| A | ASP91 | |
| A | LEU113 | |
| A | TYR128 | |
| A | LYS189 | |
| A | HIS215 | |
| A | ARG220 | |
| B | GLY35 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 14 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:12501186 |
| Chain | Residue | Details |
| A | SER117 | |
| B | TYR185 | |
| B | ASN214 | |
| B | GLY247 | |
| B | ARG253 | |
| B | ARG314 | |
| A | SER162 | |
| 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 | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR185 | |
| B | 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 | CSA3 |
| 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 | CSA4 |
| 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 | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR185 | |
| A | LYS189 | |
| A | SER162 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR185 | |
| B | LYS189 | |
| B | SER162 |
| site_id | CSA7 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | ARG182 | |
| A | LYS189 |
| site_id | CSA8 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | ARG182 | |
| B | LYS189 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR185 | |
| A | LYS189 |
