5IN4
Crystal Structure of GDP-mannose 4,6 dehydratase bound to a GDP-fucose based inhibitor
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 | 41 |
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 | HOH1108 |
A | HOH1183 |
A | HOH1212 |
A | HOH1213 |
A | HOH1214 |
A | GLY33 |
A | HOH1217 |
A | HOH1234 |
A | HOH1253 |
A | HOH1255 |
A | HOH1282 |
A | HOH1310 |
A | HOH1319 |
A | HOH1328 |
B | ARG56 |
B | SER57 |
A | GLN34 |
B | SER58 |
B | HOH711 |
A | ASP35 |
A | ARG55 |
A | ASN61 |
A | ASP86 |
A | LEU87 |
site_id | AC2 |
Number of Residues | 21 |
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 | HOH1130 |
A | HOH1161 |
A | HOH1260 |
A | HOH1266 |
B | HOH574 |
site_id | AC3 |
Number of Residues | 21 |
Details | binding site for residue 6CK A 1003 |
Chain | Residue |
A | PHE60 |
A | THR62 |
A | TYR69 |
A | HIS75 |
A | GLU77 |
A | LEU82 |
A | TYR84 |
A | HOH1112 |
A | HOH1153 |
A | HOH1167 |
A | HOH1178 |
A | HOH1197 |
A | HOH1211 |
A | HOH1224 |
A | HOH1237 |
B | ALA216 |
B | ASN217 |
B | LYS222 |
B | ARG225 |
B | TYR323 |
B | ALA372 |
site_id | AC4 |
Number of Residues | 25 |
Details | binding site for residue 6CK B 401 |
Chain | Residue |
B | HOH580 |
B | HOH582 |
B | HOH593 |
B | HOH622 |
B | HOH629 |
B | HOH659 |
B | HOH668 |
B | HOH739 |
B | HOH746 |
A | ALA216 |
A | ASN217 |
A | LYS222 |
A | ARG225 |
A | TYR323 |
A | ALA372 |
B | VAL54 |
B | PHE60 |
B | THR62 |
B | TYR69 |
B | HIS75 |
B | GLU77 |
B | LEU82 |
B | TYR84 |
B | HOH510 |
B | HOH574 |
site_id | AC5 |
Number of Residues | 39 |
Details | binding site for residue NAP B 402 |
Chain | Residue |
A | ARG56 |
A | SER57 |
A | SER58 |
A | HOH1209 |
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 | HOH528 |
B | HOH602 |
B | HOH605 |
B | HOH619 |
B | HOH652 |
B | HOH658 |
B | HOH660 |
B | HOH674 |
B | HOH688 |
B | HOH702 |
B | HOH726 |
site_id | AC6 |
Number of Residues | 23 |
Details | binding site for residue GDP B 403 |
Chain | Residue |
A | HOH1178 |
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 | HOH522 |
B | HOH525 |
B | HOH527 |
B | HOH531 |
B | HOH620 |
B | HOH654 |
site_id | AC7 |
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 | HOH1141 |
C | HOH1148 |
C | HOH1193 |
C | HOH1226 |
C | HOH1255 |
C | HOH1257 |
C | HOH1264 |
C | HOH1273 |
C | HOH1281 |
C | HOH1283 |
C | HOH1285 |
C | HOH1336 |
D | ARG56 |
D | SER57 |
D | SER58 |
D | HOH754 |
site_id | AC8 |
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 | HOH1115 |
C | HOH1220 |
C | HOH1270 |
C | HOH1277 |
C | HOH1344 |
D | HOH584 |
site_id | AC9 |
Number of Residues | 24 |
Details | binding site for residue 6CK C 1003 |
Chain | Residue |
C | PHE60 |
C | THR62 |
C | TYR69 |
C | HIS75 |
C | GLU77 |
C | LEU82 |
C | TYR84 |
C | HOH1113 |
C | HOH1144 |
C | HOH1149 |
C | HOH1196 |
C | HOH1239 |
C | HOH1242 |
C | HOH1244 |
C | HOH1340 |
C | HOH1352 |
C | HOH1356 |
D | ALA216 |
D | ASN217 |
D | LYS222 |
D | ARG225 |
D | TYR323 |
D | ALA372 |
D | HOH626 |
site_id | AD1 |
Number of Residues | 23 |
Details | binding site for residue 6CK D 401 |
Chain | Residue |
C | ALA216 |
C | ASN217 |
C | LYS222 |
C | ARG225 |
C | TYR323 |
C | ALA372 |
D | PHE60 |
D | THR62 |
D | TYR69 |
D | HIS75 |
D | GLU77 |
D | LEU82 |
D | TYR84 |
D | HOH527 |
D | HOH556 |
D | HOH570 |
D | HOH584 |
D | HOH594 |
D | HOH625 |
D | HOH647 |
D | HOH675 |
D | HOH689 |
D | HOH781 |
site_id | AD2 |
Number of Residues | 40 |
Details | binding site for residue NAP D 402 |
Chain | Residue |
C | ARG56 |
C | SER57 |
C | SER58 |
C | HOH1136 |
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 | HOH558 |
D | HOH571 |
D | HOH595 |
D | HOH634 |
D | HOH643 |
D | HOH659 |
D | HOH672 |
D | HOH680 |
D | HOH692 |
D | HOH724 |
D | HOH732 |
D | HOH764 |
site_id | AD3 |
Number of Residues | 22 |
Details | binding site for residue GDP D 403 |
Chain | Residue |
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 | HOH559 |
D | HOH569 |
D | HOH626 |
D | HOH687 |
D | HOH695 |
D | HOH715 |
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 | ACT_SITE: ACT_SITE => ECO:0000250 |
Chain | Residue | Details |
A | THR155 | |
B | THR155 | |
C | THR155 | |
D | THR155 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | ACT_SITE: Nucleophile => ECO:0000250 |
Chain | Residue | Details |
A | GLU157 | |
A | TYR179 | |
B | GLU157 | |
B | TYR179 | |
C | GLU157 | |
C | TYR179 | |
D | GLU157 | |
D | TYR179 |
site_id | SWS_FT_FI3 |
Number of Residues | 32 |
Details | BINDING: BINDING => ECO:0000269|Ref.9 |
Chain | Residue | Details |
A | GLY30 | |
B | ARG55 | |
B | ASP86 | |
B | LEU108 | |
B | TYR123 | |
B | LYS183 | |
B | HIS209 | |
B | ARG214 | |
C | GLY30 | |
C | ARG55 | |
C | ASP86 | |
A | ARG55 | |
C | LEU108 | |
C | TYR123 | |
C | LYS183 | |
C | HIS209 | |
C | ARG214 | |
D | GLY30 | |
D | ARG55 | |
D | ASP86 | |
D | LEU108 | |
D | TYR123 | |
A | ASP86 | |
D | LYS183 | |
D | HIS209 | |
D | ARG214 | |
A | LEU108 | |
A | TYR123 | |
A | LYS183 | |
A | HIS209 | |
A | ARG214 | |
B | GLY30 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
A | TYR323 | |
B | TYR323 | |
C | TYR323 | |
D | TYR323 |