5IN5
Crystal Structure of GDP-mannose 4,6 dehydratase in complex with natural inhibitor GDP-Fucose
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 | 40 |
| Details | binding site for residue NAP A 1001 |
| Chain | Residue |
| A | GLY30 |
| A | LEU108 |
| A | GLY109 |
| A | ALA110 |
| A | SER112 |
| A | TYR123 |
| A | VAL127 |
| A | ALA153 |
| A | SER154 |
| A | THR155 |
| A | TYR179 |
| A | THR32 |
| A | LYS183 |
| A | LEU206 |
| A | ASN208 |
| A | HIS209 |
| A | ARG214 |
| A | HOH1167 |
| A | HOH1168 |
| A | HOH1169 |
| A | HOH1190 |
| A | HOH1206 |
| A | GLY33 |
| A | HOH1224 |
| A | HOH1236 |
| A | HOH1240 |
| A | HOH1243 |
| A | HOH1269 |
| A | HOH1285 |
| A | HOH1338 |
| B | ARG56 |
| B | SER57 |
| B | SER58 |
| A | GLN34 |
| B | HOH539 |
| A | ASP35 |
| A | ARG55 |
| A | ASN61 |
| A | ASP86 |
| A | LEU87 |
| site_id | AC2 |
| Number of Residues | 22 |
| Details | binding site for residue GDP A 1002 |
| Chain | Residue |
| A | VAL114 |
| A | GLU157 |
| 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 | HOH1175 |
| A | HOH1180 |
| A | HOH1231 |
| A | HOH1244 |
| A | HOH1296 |
| A | HOH1318 |
| site_id | AC3 |
| Number of Residues | 21 |
| Details | binding site for residue GFB A 1003 |
| Chain | Residue |
| A | PHE60 |
| A | THR62 |
| A | GLU66 |
| A | TYR69 |
| A | HIS75 |
| A | GLU77 |
| A | LEU82 |
| A | TYR84 |
| A | HOH1136 |
| A | HOH1173 |
| A | HOH1182 |
| A | HOH1249 |
| A | HOH1258 |
| A | HOH1273 |
| A | HOH1316 |
| B | ALA216 |
| B | ASN217 |
| B | LYS222 |
| B | ARG225 |
| B | TYR323 |
| B | ALA372 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue GOL A 1004 |
| Chain | Residue |
| A | TYR231 |
| A | HIS291 |
| A | HIS360 |
| site_id | AC5 |
| Number of Residues | 22 |
| Details | binding site for residue GFB B 401 |
| Chain | Residue |
| B | GLU77 |
| B | LEU82 |
| B | TYR84 |
| B | HOH522 |
| B | HOH525 |
| B | HOH537 |
| B | HOH554 |
| B | HOH613 |
| B | HOH734 |
| A | ALA216 |
| A | ASN217 |
| A | LYS222 |
| A | ARG225 |
| A | TYR323 |
| A | ALA372 |
| A | HOH1175 |
| B | PHE60 |
| B | THR62 |
| B | GLU66 |
| B | TYR69 |
| B | ALA74 |
| B | HIS75 |
| site_id | AC6 |
| Number of Residues | 39 |
| Details | binding site for residue NAP B 402 |
| Chain | Residue |
| A | ARG56 |
| A | SER57 |
| A | SER58 |
| A | HOH1133 |
| A | HOH1274 |
| B | GLY30 |
| B | THR32 |
| B | GLY33 |
| B | GLN34 |
| B | ASP35 |
| B | ARG55 |
| B | ASN61 |
| 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 | HOH526 |
| B | HOH548 |
| B | HOH589 |
| B | HOH590 |
| B | HOH625 |
| B | HOH630 |
| B | HOH655 |
| B | HOH657 |
| B | HOH677 |
| B | HOH716 |
| site_id | AC7 |
| Number of Residues | 22 |
| Details | binding site for residue GDP B 403 |
| Chain | Residue |
| A | HOH1173 |
| B | VAL114 |
| B | GLU157 |
| B | ASN208 |
| B | ASN217 |
| B | PHE218 |
| B | VAL219 |
| B | LYS222 |
| B | LEU240 |
| B | GLY241 |
| B | ASN242 |
| B | ALA245 |
| B | ARG247 |
| B | VAL281 |
| B | TYR323 |
| B | ARG325 |
| B | GLU328 |
| B | HOH512 |
| B | HOH563 |
| B | HOH614 |
| B | HOH678 |
| B | HOH704 |
| site_id | AC8 |
| Number of Residues | 40 |
| Details | binding site for residue NAP C 1001 |
| Chain | Residue |
| C | GLY30 |
| C | THR32 |
| C | GLY33 |
| C | GLN34 |
| C | ASP35 |
| C | ARG55 |
| C | ASN61 |
| 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 | HOH1140 |
| C | HOH1141 |
| C | HOH1144 |
| C | HOH1151 |
| C | HOH1210 |
| C | HOH1211 |
| C | HOH1216 |
| C | HOH1225 |
| C | HOH1257 |
| C | HOH1291 |
| C | HOH1303 |
| C | HOH1313 |
| C | HOH1314 |
| D | ARG56 |
| D | SER57 |
| D | SER58 |
| site_id | AC9 |
| Number of Residues | 22 |
| Details | binding site for residue GDP C 1002 |
| Chain | Residue |
| C | VAL114 |
| C | GLU157 |
| C | ASN208 |
| C | ASN217 |
| C | PHE218 |
| C | VAL219 |
| C | LYS222 |
| C | LEU240 |
| C | GLY241 |
| C | ASN242 |
| C | ALA245 |
| C | ARG247 |
| C | VAL281 |
| C | TYR323 |
| C | ARG325 |
| C | GLU328 |
| C | HOH1124 |
| C | HOH1150 |
| C | HOH1221 |
| C | HOH1242 |
| C | HOH1288 |
| D | HOH555 |
| site_id | AD1 |
| Number of Residues | 23 |
| Details | binding site for residue GFB C 1003 |
| Chain | Residue |
| C | PHE60 |
| C | THR62 |
| C | GLU66 |
| C | TYR69 |
| C | ALA74 |
| C | HIS75 |
| C | GLU77 |
| C | LEU82 |
| C | TYR84 |
| C | HOH1121 |
| C | HOH1135 |
| C | HOH1175 |
| C | HOH1201 |
| C | HOH1207 |
| C | HOH1323 |
| C | HOH1333 |
| D | ALA216 |
| D | ASN217 |
| D | LYS222 |
| D | ARG225 |
| D | TYR323 |
| D | ALA372 |
| D | HOH547 |
| site_id | AD2 |
| Number of Residues | 23 |
| Details | binding site for residue GFB D 401 |
| Chain | Residue |
| C | ALA216 |
| C | ASN217 |
| C | LYS222 |
| C | ARG225 |
| C | TYR323 |
| C | ALA372 |
| D | PHE60 |
| D | THR62 |
| D | GLU66 |
| D | TYR69 |
| D | HIS75 |
| D | GLU77 |
| D | LEU82 |
| D | TYR84 |
| D | HOH553 |
| D | HOH555 |
| D | HOH570 |
| D | HOH612 |
| D | HOH624 |
| D | HOH628 |
| D | HOH652 |
| D | HOH705 |
| D | HOH730 |
| site_id | AD3 |
| Number of Residues | 39 |
| Details | binding site for residue NAP D 402 |
| Chain | Residue |
| C | ARG56 |
| C | SER57 |
| C | SER58 |
| D | GLY30 |
| D | THR32 |
| D | GLY33 |
| D | GLN34 |
| D | ASP35 |
| D | ARG55 |
| D | ASN61 |
| 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 | HOH538 |
| D | HOH560 |
| D | HOH562 |
| D | HOH574 |
| D | HOH606 |
| D | HOH615 |
| D | HOH627 |
| D | HOH656 |
| D | HOH672 |
| D | HOH677 |
| D | HOH681 |
| D | HOH722 |
| site_id | AD4 |
| Number of Residues | 22 |
| Details | binding site for residue GDP D 403 |
| Chain | Residue |
| C | HOH1175 |
| 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 | HOH537 |
| D | HOH563 |
| D | HOH646 |
| D | HOH666 |
| D | HOH683 |
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 |
