1RPN
Crystal Structure of GDP-D-mannose 4,6-dehydratase in complexes with GDP and NADPH
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| A | 0009103 | biological_process | lipopolysaccharide biosynthetic process |
| A | 0009243 | biological_process | O antigen biosynthetic process |
| A | 0016829 | molecular_function | lyase activity |
| A | 0019306 | biological_process | GDP-D-rhamnose biosynthetic process |
| A | 0019673 | biological_process | GDP-mannose metabolic process |
| A | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| A | 0070401 | molecular_function | NADP+ binding |
| B | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| B | 0009103 | biological_process | lipopolysaccharide biosynthetic process |
| B | 0009243 | biological_process | O antigen biosynthetic process |
| B | 0016829 | molecular_function | lyase activity |
| B | 0019306 | biological_process | GDP-D-rhamnose biosynthetic process |
| B | 0019673 | biological_process | GDP-mannose metabolic process |
| B | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| B | 0070401 | molecular_function | NADP+ binding |
| C | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| C | 0009103 | biological_process | lipopolysaccharide biosynthetic process |
| C | 0009243 | biological_process | O antigen biosynthetic process |
| C | 0016829 | molecular_function | lyase activity |
| C | 0019306 | biological_process | GDP-D-rhamnose biosynthetic process |
| C | 0019673 | biological_process | GDP-mannose metabolic process |
| C | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| C | 0070401 | molecular_function | NADP+ binding |
| D | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| D | 0009103 | biological_process | lipopolysaccharide biosynthetic process |
| D | 0009243 | biological_process | O antigen biosynthetic process |
| D | 0016829 | molecular_function | lyase activity |
| D | 0019306 | biological_process | GDP-D-rhamnose biosynthetic process |
| D | 0019673 | biological_process | GDP-mannose metabolic process |
| D | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
| D | 0070401 | molecular_function | NADP+ binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 40 |
| Details | BINDING SITE FOR RESIDUE NDP A 1501 |
| Chain | Residue |
| A | GLY9 |
| A | LEU81 |
| A | ALA82 |
| A | ALA83 |
| A | SER85 |
| A | VAL100 |
| A | ALA124 |
| A | SER125 |
| A | THR126 |
| A | TYR150 |
| A | LYS154 |
| A | THR11 |
| A | LEU177 |
| A | ASN179 |
| A | HIS180 |
| A | ARG185 |
| A | HOH1604 |
| A | HOH1609 |
| A | HOH1613 |
| A | HOH1617 |
| A | HOH1618 |
| A | HOH1620 |
| A | GLY12 |
| A | HOH1622 |
| A | HOH1637 |
| A | HOH1641 |
| A | HOH1650 |
| A | HOH1660 |
| A | HOH1673 |
| A | HOH1698 |
| A | HOH1723 |
| D | ARG35 |
| D | ARG36 |
| A | GLN13 |
| D | SER37 |
| A | ASP14 |
| A | ALA34 |
| A | ARG36 |
| A | ASP59 |
| A | MET60 |
| site_id | AC2 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP B 1502 |
| Chain | Residue |
| B | GLY9 |
| B | THR11 |
| B | GLY12 |
| B | GLN13 |
| B | ASP14 |
| B | ALA34 |
| B | ARG36 |
| B | ASP59 |
| B | MET60 |
| B | LEU81 |
| B | ALA82 |
| B | ALA83 |
| B | SER85 |
| B | VAL100 |
| B | ALA124 |
| B | SER125 |
| B | THR126 |
| B | TYR150 |
| B | LYS154 |
| B | LEU177 |
| B | ASN179 |
| B | HIS180 |
| B | ARG185 |
| B | HOH1609 |
| B | HOH1611 |
| B | HOH1615 |
| B | HOH1620 |
| B | HOH1622 |
| B | HOH1624 |
| B | HOH1630 |
| B | HOH1640 |
| B | HOH1641 |
| B | HOH1654 |
| B | HOH1663 |
| B | HOH1687 |
| B | HOH1694 |
| C | ARG35 |
| C | ARG36 |
| C | SER37 |
| site_id | AC3 |
| Number of Residues | 41 |
| Details | BINDING SITE FOR RESIDUE NDP C 1503 |
| Chain | Residue |
| C | TYR150 |
| C | LYS154 |
| C | LEU177 |
| C | ASN179 |
| C | HIS180 |
| C | ARG185 |
| C | HOH1613 |
| C | HOH1615 |
| C | HOH1622 |
| C | HOH1623 |
| C | HOH1624 |
| C | HOH1632 |
| C | HOH1634 |
| C | HOH1643 |
| C | HOH1644 |
| C | HOH1648 |
| C | HOH1664 |
| C | HOH1696 |
| C | HOH1702 |
| C | HOH1717 |
| C | HOH1729 |
| B | ARG35 |
| B | ARG36 |
| B | SER37 |
| C | GLY9 |
| C | THR11 |
| C | GLY12 |
| C | GLN13 |
| C | ASP14 |
| C | ALA34 |
| C | ARG36 |
| C | ASP59 |
| C | MET60 |
| C | LEU81 |
| C | ALA82 |
| C | ALA83 |
| C | SER85 |
| C | VAL100 |
| C | ALA124 |
| C | SER125 |
| C | THR126 |
| site_id | AC4 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP D 1504 |
| Chain | Residue |
| A | ARG35 |
| A | ARG36 |
| A | SER37 |
| A | HOH1682 |
| D | GLY9 |
| D | THR11 |
| D | GLY12 |
| D | GLN13 |
| D | ASP14 |
| D | ALA34 |
| D | ARG36 |
| D | ASP59 |
| D | MET60 |
| D | LEU81 |
| D | ALA82 |
| D | ALA83 |
| D | SER85 |
| D | VAL100 |
| D | ALA124 |
| D | SER125 |
| D | THR126 |
| D | TYR150 |
| D | LYS154 |
| D | LEU177 |
| D | ASN179 |
| D | HIS180 |
| D | ARG185 |
| D | HOH1614 |
| D | HOH1617 |
| D | HOH1619 |
| D | HOH1624 |
| D | HOH1626 |
| D | HOH1635 |
| D | HOH1637 |
| D | HOH1647 |
| D | HOH1681 |
| D | HOH1684 |
| D | HOH1694 |
| D | HOH1717 |
| site_id | AC5 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE GDP A 1601 |
| Chain | Residue |
| A | PHE86 |
| A | VAL87 |
| A | GLU128 |
| A | ASN179 |
| A | GLU188 |
| A | PHE189 |
| A | VAL190 |
| A | LYS193 |
| A | LEU211 |
| A | GLY212 |
| A | ASN213 |
| A | ALA216 |
| A | ARG218 |
| A | VAL252 |
| A | PHE277 |
| A | ARG279 |
| A | GLU282 |
| A | VAL283 |
| A | HOH1615 |
| A | HOH1616 |
| A | HOH1633 |
| A | HOH1638 |
| A | HOH1670 |
| A | HOH1679 |
| A | HOH1723 |
| site_id | AC6 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE GDP B 1602 |
| Chain | Residue |
| B | PHE86 |
| B | VAL87 |
| B | GLU128 |
| B | ASN179 |
| B | GLU188 |
| B | PHE189 |
| B | VAL190 |
| B | LYS193 |
| B | LEU211 |
| B | GLY212 |
| B | ASN213 |
| B | ALA216 |
| B | ARG218 |
| B | VAL252 |
| B | PHE277 |
| B | ARG279 |
| B | GLU282 |
| B | HOH1608 |
| B | HOH1635 |
| B | HOH1643 |
| B | HOH1647 |
| B | HOH1657 |
| B | HOH1664 |
| site_id | AC7 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE GDP C 1603 |
| Chain | Residue |
| C | PHE86 |
| C | VAL87 |
| C | GLU128 |
| C | ASN179 |
| C | GLU188 |
| C | PHE189 |
| C | VAL190 |
| C | LYS193 |
| C | LEU211 |
| C | GLY212 |
| C | ASN213 |
| C | ALA216 |
| C | ARG218 |
| C | VAL252 |
| C | PHE277 |
| C | ARG279 |
| C | GLU282 |
| C | HOH1608 |
| C | HOH1614 |
| C | HOH1635 |
| C | HOH1640 |
| C | HOH1646 |
| C | HOH1693 |
| site_id | AC8 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE GDP D 1604 |
| Chain | Residue |
| D | PHE86 |
| D | GLU128 |
| D | ASN179 |
| D | GLU188 |
| D | PHE189 |
| D | VAL190 |
| D | LYS193 |
| D | LEU211 |
| D | GLY212 |
| D | ASN213 |
| D | ALA216 |
| D | ARG218 |
| D | VAL252 |
| D | PHE277 |
| D | ARG279 |
| D | GLU282 |
| D | HOH1611 |
| D | HOH1612 |
| D | HOH1652 |
| D | HOH1655 |
| D | HOH1678 |
| D | HOH1679 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00955","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Active site: {"description":"Nucleophile","evidences":[{"source":"HAMAP-Rule","id":"MF_00955","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 48 |
| Details | Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00955","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"14739333","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | THR126 | |
| A | LYS154 | |
| A | TYR150 | |
| A | GLU128 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | LYS154 | |
| B | ARG147 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | LYS154 | |
| C | ARG147 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | THR126 | |
| B | LYS154 | |
| B | TYR150 | |
| B | GLU128 |
| site_id | CSA3 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | THR126 | |
| C | LYS154 | |
| C | TYR150 | |
| C | GLU128 |
| site_id | CSA4 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | THR126 | |
| D | LYS154 | |
| D | TYR150 | |
| D | GLU128 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | THR126 | |
| A | LYS154 | |
| A | TYR150 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | THR126 | |
| B | LYS154 | |
| B | TYR150 |
| site_id | CSA7 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | THR126 | |
| C | LYS154 | |
| C | TYR150 |
| site_id | CSA8 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | THR126 | |
| D | LYS154 | |
| D | TYR150 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | LYS154 | |
| A | ARG147 |
