1T2A
Crystal structure of human GDP-D-mannose 4,6-dehydratase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005515 | molecular_function | protein binding |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0007219 | biological_process | Notch signaling pathway |
| A | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| 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 |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0070062 | cellular_component | extracellular exosome |
| A | 0070401 | molecular_function | NADP+ binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0007219 | biological_process | Notch signaling pathway |
| B | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| 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 |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0070062 | cellular_component | extracellular exosome |
| B | 0070401 | molecular_function | NADP+ binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0007219 | biological_process | Notch signaling pathway |
| C | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| 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 |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0070062 | cellular_component | extracellular exosome |
| C | 0070401 | molecular_function | NADP+ binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0007219 | biological_process | Notch signaling pathway |
| D | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
| 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 |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0070062 | cellular_component | extracellular exosome |
| D | 0070401 | molecular_function | NADP+ binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP A 1001 |
| Chain | Residue |
| A | GLY30 |
| A | GLY109 |
| A | ALA110 |
| A | SER112 |
| A | TYR123 |
| A | VAL127 |
| A | ALA153 |
| A | SER154 |
| A | THR155 |
| A | TYR179 |
| A | LYS183 |
| A | THR32 |
| A | LEU206 |
| A | ASN208 |
| A | HIS209 |
| A | ARG214 |
| A | HOH1004 |
| A | HOH1010 |
| A | HOH1013 |
| A | HOH1015 |
| A | HOH1017 |
| A | HOH1021 |
| A | GLY33 |
| A | HOH1031 |
| A | HOH1039 |
| A | HOH1059 |
| A | HOH1071 |
| A | HOH1147 |
| A | HOH1190 |
| D | ARG56 |
| D | SER57 |
| D | SER58 |
| D | HOH1320 |
| A | GLN34 |
| A | ASP35 |
| A | ARG55 |
| A | ASP86 |
| A | LEU87 |
| A | LEU108 |
| site_id | AC2 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE GDP A 1002 |
| Chain | Residue |
| A | VAL114 |
| A | ASN208 |
| A | ASN217 |
| A | PHE218 |
| A | VAL219 |
| A | LYS222 |
| A | LEU240 |
| A | GLY241 |
| A | ASN242 |
| A | ALA245 |
| A | ARG247 |
| A | VAL281 |
| A | TYR323 |
| A | ARG325 |
| A | GLU328 |
| A | HOH1011 |
| A | HOH1036 |
| A | HOH1042 |
| A | HOH1045 |
| A | HOH1046 |
| A | HOH1064 |
| A | HOH1174 |
| site_id | AC3 |
| Number of Residues | 37 |
| Details | BINDING SITE FOR RESIDUE NDP B 1101 |
| Chain | Residue |
| B | GLY30 |
| B | THR32 |
| B | GLY33 |
| B | GLN34 |
| B | ASP35 |
| B | ARG55 |
| B | ASP86 |
| B | LEU87 |
| B | LEU108 |
| B | GLY109 |
| B | ALA110 |
| B | SER112 |
| B | TYR123 |
| B | VAL127 |
| B | ALA153 |
| B | SER154 |
| B | THR155 |
| B | TYR179 |
| B | LYS183 |
| B | LEU206 |
| B | ASN208 |
| B | HIS209 |
| B | ARG214 |
| B | HOH1111 |
| B | HOH1113 |
| B | HOH1119 |
| B | HOH1128 |
| B | HOH1131 |
| B | HOH1132 |
| B | HOH1152 |
| B | HOH1196 |
| B | HOH1256 |
| B | HOH1271 |
| B | HOH1341 |
| C | ARG56 |
| C | SER58 |
| C | HOH1244 |
| site_id | AC4 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE GDP B 1102 |
| Chain | Residue |
| B | GLU157 |
| B | ASN208 |
| B | ASN217 |
| B | VAL219 |
| B | LYS222 |
| B | LEU240 |
| B | GLY241 |
| B | ASN242 |
| B | ALA245 |
| B | ARG247 |
| B | VAL281 |
| B | ARG325 |
| B | GLU328 |
| B | HOH1109 |
| B | HOH1122 |
| B | HOH1129 |
| B | HOH1133 |
| B | HOH1223 |
| B | HOH1274 |
| B | HIS113 |
| site_id | AC5 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP C 1201 |
| Chain | Residue |
| B | ARG56 |
| B | SER57 |
| B | SER58 |
| C | GLY30 |
| C | THR32 |
| C | GLY33 |
| C | GLN34 |
| C | ASP35 |
| C | ARG55 |
| C | ASP86 |
| C | LEU87 |
| C | LEU108 |
| C | GLY109 |
| C | ALA110 |
| C | SER112 |
| C | TYR123 |
| C | VAL127 |
| C | ALA153 |
| C | SER154 |
| C | THR155 |
| C | TYR179 |
| C | LYS183 |
| C | LEU206 |
| C | ASN208 |
| C | HIS209 |
| C | ARG214 |
| C | HOH1205 |
| C | HOH1206 |
| C | HOH1210 |
| C | HOH1211 |
| C | HOH1213 |
| C | HOH1217 |
| C | HOH1227 |
| C | HOH1230 |
| C | HOH1235 |
| C | HOH1316 |
| C | HOH1341 |
| C | HOH1344 |
| C | HOH1345 |
| site_id | AC6 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE GDP C 1202 |
| Chain | Residue |
| C | VAL114 |
| C | GLU157 |
| C | ASN208 |
| C | ASN217 |
| C | VAL219 |
| C | LYS222 |
| C | LEU240 |
| C | GLY241 |
| C | ASN242 |
| C | ALA245 |
| C | ARG247 |
| C | VAL281 |
| C | TYR323 |
| C | ARG325 |
| C | GLU328 |
| C | HOH1226 |
| C | HOH1232 |
| C | HOH1236 |
| C | HOH1241 |
| C | HOH1250 |
| C | HOH1300 |
| C | HOH1334 |
| site_id | AC7 |
| Number of Residues | 39 |
| Details | BINDING SITE FOR RESIDUE NDP D 1301 |
| Chain | Residue |
| A | ARG56 |
| A | SER57 |
| A | SER58 |
| A | HOH1205 |
| D | GLY30 |
| D | THR32 |
| D | GLY33 |
| D | GLN34 |
| D | ASP35 |
| D | ARG55 |
| D | ASP86 |
| D | LEU87 |
| D | LEU108 |
| D | GLY109 |
| D | ALA110 |
| D | SER112 |
| D | TYR123 |
| D | VAL127 |
| D | ALA153 |
| D | SER154 |
| D | THR155 |
| D | TYR179 |
| D | LYS183 |
| D | LEU206 |
| D | ASN208 |
| D | HIS209 |
| D | ARG214 |
| D | HOH1303 |
| D | HOH1304 |
| D | HOH1307 |
| D | HOH1316 |
| D | HOH1321 |
| D | HOH1330 |
| D | HOH1343 |
| D | HOH1344 |
| D | HOH1345 |
| D | HOH1367 |
| D | HOH1461 |
| D | HOH1483 |
| site_id | AC8 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE GDP D 1302 |
| Chain | Residue |
| D | HIS113 |
| D | VAL114 |
| D | GLU157 |
| D | ASN208 |
| D | ASN217 |
| D | PHE218 |
| D | VAL219 |
| D | LYS222 |
| D | LEU240 |
| D | GLY241 |
| D | ASN242 |
| D | ALA245 |
| D | ARG247 |
| D | VAL281 |
| D | TYR323 |
| D | ARG325 |
| D | GLU328 |
| D | HOH1312 |
| D | HOH1317 |
| D | HOH1318 |
| D | HOH1327 |
| D | HOH1348 |
| D | HOH1376 |
| D | HOH1425 |
Functional Information from PROSITE/UniProt
| site_id | PS00061 |
| Number of Residues | 29 |
| Details | ADH_SHORT Short-chain dehydrogenases/reductases family signature. PqkettpfypRspYGAAKLYAyWIVvNFR |
| Chain | Residue | Details |
| A | PRO166-ARG194 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | Active site: {"evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | Active site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000250"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 68 |
| Details | Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2004","submissionDatabase":"PDB data bank","title":"Crystal structure and biophysical characterization of human GDP-D-mannose 4,6-dehydratase.","authors":["Vedadi M.","Walker J.R.","Sharma S.","Houston S.","Wasney G.","Loppnau P.","Oppermann U."]}}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]} |
| 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 | TYR179 | |
| A | THR155 | |
| A | LYS183 | |
| A | GLU157 |
| site_id | CSA10 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR179 | |
| B | LYS183 |
| site_id | CSA11 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | TYR179 | |
| C | LYS183 |
| site_id | CSA12 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | TYR179 | |
| D | LYS183 |
| site_id | CSA2 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | TYR179 | |
| B | THR155 | |
| B | LYS183 | |
| B | GLU157 |
| site_id | CSA3 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | TYR179 | |
| C | THR155 | |
| C | LYS183 | |
| C | GLU157 |
| site_id | CSA4 |
| Number of Residues | 4 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | TYR179 | |
| D | THR155 | |
| D | LYS183 | |
| D | GLU157 |
| site_id | CSA5 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | THR155 | |
| A | TYR179 | |
| A | LYS183 |
| site_id | CSA6 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| B | THR155 | |
| B | TYR179 | |
| B | LYS183 |
| site_id | CSA7 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| C | THR155 | |
| C | TYR179 | |
| C | LYS183 |
| site_id | CSA8 |
| Number of Residues | 3 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| D | THR155 | |
| D | TYR179 | |
| D | LYS183 |
| site_id | CSA9 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1db3 |
| Chain | Residue | Details |
| A | TYR179 | |
| A | LYS183 |
