4B8Z
Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral crystal form
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005515 | molecular_function | protein binding |
A | 0005829 | cellular_component | cytosol |
A | 0007159 | biological_process | leukocyte cell-cell adhesion |
A | 0009055 | molecular_function | electron transfer activity |
A | 0009226 | biological_process | nucleotide-sugar biosynthetic process |
A | 0010595 | biological_process | positive regulation of endothelial cell migration |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016853 | molecular_function | isomerase activity |
A | 0019673 | biological_process | GDP-mannose metabolic process |
A | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
A | 0042356 | molecular_function | GDP-4-dehydro-D-rhamnose reductase activity |
A | 0042802 | molecular_function | identical protein binding |
A | 0047918 | molecular_function | GDP-mannose 3,5-epimerase activity |
A | 0050577 | molecular_function | GDP-L-fucose synthase activity |
A | 0070062 | cellular_component | extracellular exosome |
A | 1904906 | biological_process | positive regulation of endothelial cell-matrix adhesion via fibronectin |
B | 0005515 | molecular_function | protein binding |
B | 0005829 | cellular_component | cytosol |
B | 0007159 | biological_process | leukocyte cell-cell adhesion |
B | 0009055 | molecular_function | electron transfer activity |
B | 0009226 | biological_process | nucleotide-sugar biosynthetic process |
B | 0010595 | biological_process | positive regulation of endothelial cell migration |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016853 | molecular_function | isomerase activity |
B | 0019673 | biological_process | GDP-mannose metabolic process |
B | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
B | 0042356 | molecular_function | GDP-4-dehydro-D-rhamnose reductase activity |
B | 0042802 | molecular_function | identical protein binding |
B | 0047918 | molecular_function | GDP-mannose 3,5-epimerase activity |
B | 0050577 | molecular_function | GDP-L-fucose synthase activity |
B | 0070062 | cellular_component | extracellular exosome |
B | 1904906 | biological_process | positive regulation of endothelial cell-matrix adhesion via fibronectin |
C | 0005515 | molecular_function | protein binding |
C | 0005829 | cellular_component | cytosol |
C | 0007159 | biological_process | leukocyte cell-cell adhesion |
C | 0009055 | molecular_function | electron transfer activity |
C | 0009226 | biological_process | nucleotide-sugar biosynthetic process |
C | 0010595 | biological_process | positive regulation of endothelial cell migration |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016853 | molecular_function | isomerase activity |
C | 0019673 | biological_process | GDP-mannose metabolic process |
C | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
C | 0042356 | molecular_function | GDP-4-dehydro-D-rhamnose reductase activity |
C | 0042802 | molecular_function | identical protein binding |
C | 0047918 | molecular_function | GDP-mannose 3,5-epimerase activity |
C | 0050577 | molecular_function | GDP-L-fucose synthase activity |
C | 0070062 | cellular_component | extracellular exosome |
C | 1904906 | biological_process | positive regulation of endothelial cell-matrix adhesion via fibronectin |
D | 0005515 | molecular_function | protein binding |
D | 0005829 | cellular_component | cytosol |
D | 0007159 | biological_process | leukocyte cell-cell adhesion |
D | 0009055 | molecular_function | electron transfer activity |
D | 0009226 | biological_process | nucleotide-sugar biosynthetic process |
D | 0010595 | biological_process | positive regulation of endothelial cell migration |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016853 | molecular_function | isomerase activity |
D | 0019673 | biological_process | GDP-mannose metabolic process |
D | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
D | 0042356 | molecular_function | GDP-4-dehydro-D-rhamnose reductase activity |
D | 0042802 | molecular_function | identical protein binding |
D | 0047918 | molecular_function | GDP-mannose 3,5-epimerase activity |
D | 0050577 | molecular_function | GDP-L-fucose synthase activity |
D | 0070062 | cellular_component | extracellular exosome |
D | 1904906 | biological_process | positive regulation of endothelial cell-matrix adhesion via fibronectin |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE NAP A 900 |
Chain | Residue |
A | GLY14 |
A | LEU48 |
A | LEU69 |
A | ALA71 |
A | VAL73 |
A | MET93 |
A | CYS112 |
A | LEU113 |
A | SER114 |
A | TYR143 |
A | LYS147 |
A | SER16 |
A | PRO170 |
A | THR171 |
A | ASN172 |
A | VAL173 |
A | GLY17 |
A | LEU18 |
A | VAL19 |
A | SER42 |
A | SER43 |
A | ALA46 |
A | ASP47 |
site_id | AC2 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE GDP A 901 |
Chain | Residue |
A | GLY75 |
A | LEU76 |
A | ASN172 |
A | GLY185 |
A | HIS186 |
A | VAL187 |
A | GLY190 |
A | LYS194 |
A | TRP208 |
A | GLY209 |
A | PRO213 |
A | ARG215 |
A | ILE252 |
A | SER276 |
A | ASP277 |
A | LYS282 |
A | HOH2003 |
site_id | AC3 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE NAP B 900 |
Chain | Residue |
B | GLY14 |
B | SER16 |
B | GLY17 |
B | LEU18 |
B | VAL19 |
B | SER42 |
B | SER43 |
B | ALA46 |
B | ASP47 |
B | LEU48 |
B | LEU69 |
B | ALA70 |
B | ALA71 |
B | VAL73 |
B | MET93 |
B | CYS112 |
B | LEU113 |
B | SER114 |
B | TYR143 |
B | LYS147 |
B | PRO170 |
B | THR171 |
B | VAL173 |
B | HIS186 |
B | ARG320 |
B | HOH2001 |
site_id | AC4 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE GDP B 901 |
Chain | Residue |
B | GLY75 |
B | LEU76 |
B | PHE77 |
B | ASN172 |
B | GLY185 |
B | HIS186 |
B | VAL187 |
B | LYS194 |
B | TRP208 |
B | GLY209 |
B | PRO213 |
B | ARG215 |
B | ILE252 |
B | SER276 |
B | ASP277 |
B | LYS282 |
site_id | AC5 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE NAP C 900 |
Chain | Residue |
C | SER114 |
C | TYR143 |
C | LYS147 |
C | PRO170 |
C | THR171 |
C | VAL173 |
C | HIS186 |
C | ARG320 |
C | HOH2001 |
C | GLY14 |
C | SER16 |
C | GLY17 |
C | LEU18 |
C | VAL19 |
C | SER42 |
C | SER43 |
C | ALA46 |
C | ASP47 |
C | LEU48 |
C | LEU69 |
C | ALA70 |
C | ALA71 |
C | VAL73 |
C | MET93 |
C | CYS112 |
C | LEU113 |
site_id | AC6 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE GDP C 901 |
Chain | Residue |
C | GLY75 |
C | LEU76 |
C | PHE77 |
C | ASN172 |
C | GLY185 |
C | HIS186 |
C | VAL187 |
C | LYS194 |
C | TRP208 |
C | GLY209 |
C | PRO213 |
C | ARG215 |
C | SER276 |
C | ASP277 |
C | LYS282 |
site_id | AC7 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE NAP D 900 |
Chain | Residue |
D | GLY14 |
D | SER16 |
D | GLY17 |
D | LEU18 |
D | VAL19 |
D | SER42 |
D | SER43 |
D | ALA46 |
D | ASP47 |
D | LEU48 |
D | LEU69 |
D | ALA70 |
D | ALA71 |
D | VAL73 |
D | MET93 |
D | CYS112 |
D | LEU113 |
D | SER114 |
D | TYR143 |
D | LYS147 |
D | PRO170 |
D | THR171 |
D | ASN172 |
D | VAL173 |
D | HIS186 |
D | ARG320 |
site_id | AC8 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE GDP D 901 |
Chain | Residue |
D | GLY75 |
D | LEU76 |
D | PHE77 |
D | ASN172 |
D | GLY185 |
D | HIS186 |
D | VAL187 |
D | LYS194 |
D | TRP208 |
D | PRO213 |
D | ARG215 |
D | SER276 |
D | ASP277 |
D | LYS282 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | ACT_SITE: Proton donor/acceptor => ECO:0000250 |
Chain | Residue | Details |
A | TYR143 | |
B | TYR143 | |
C | TYR143 | |
D | TYR143 |
site_id | SWS_FT_FI2 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:23774504, ECO:0000269|Ref.9 |
Chain | Residue | Details |
A | GLY14 | |
D | GLY14 | |
D | LYS147 | |
D | PRO170 | |
A | LYS147 | |
A | PRO170 | |
B | GLY14 | |
B | LYS147 | |
B | PRO170 | |
C | GLY14 | |
C | LYS147 | |
C | PRO170 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|Ref.9 |
Chain | Residue | Details |
A | HIS186 | |
B | HIS186 | |
C | HIS186 | |
D | HIS186 |
site_id | SWS_FT_FI4 |
Number of Residues | 16 |
Details | BINDING: BINDING => ECO:0000305|Ref.9 |
Chain | Residue | Details |
A | LYS194 | |
C | TRP208 | |
C | ARG215 | |
C | ASP277 | |
D | LYS194 | |
D | TRP208 | |
D | ARG215 | |
D | ASP277 | |
A | TRP208 | |
A | ARG215 | |
A | ASP277 | |
B | LYS194 | |
B | TRP208 | |
B | ARG215 | |
B | ASP277 | |
C | LYS194 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | SITE: Important for catalytic activity => ECO:0000250 |
Chain | Residue | Details |
A | SER114 | |
A | CYS116 | |
B | SER114 | |
B | CYS116 | |
C | SER114 | |
C | CYS116 | |
D | SER114 | |
D | CYS116 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | SITE: Lowers pKa of active site Tyr => ECO:0000250 |
Chain | Residue | Details |
A | LYS147 | |
B | LYS147 | |
C | LYS147 | |
D | LYS147 |