6GPL
Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man
Functional Information from GO Data
Chain | GOid | namespace | contents |
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 |
E | 0005515 | molecular_function | protein binding |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
E | 0007219 | biological_process | Notch signaling pathway |
E | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
E | 0016829 | molecular_function | lyase activity |
E | 0019673 | biological_process | GDP-mannose metabolic process |
E | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
E | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
E | 0042802 | molecular_function | identical protein binding |
E | 0070062 | cellular_component | extracellular exosome |
E | 0070401 | molecular_function | NADP+ binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 11 |
Details | binding site for residue BCN B 401 |
Chain | Residue |
B | ARG64 |
E | SER59 |
E | PHE60 |
B | ARG213 |
B | ARG214 |
B | GLY215 |
B | ALA216 |
B | ARG221 |
B | LEU365 |
B | HOH560 |
B | HOH695 |
site_id | AC2 |
Number of Residues | 27 |
Details | binding site for residue F7E B 402 |
Chain | Residue |
B | SER112 |
B | HIS113 |
B | VAL114 |
B | THR155 |
B | SER156 |
B | TYR179 |
B | ASN208 |
B | ARG214 |
B | ASN217 |
B | PHE218 |
B | VAL219 |
B | LYS222 |
B | LEU240 |
B | GLY241 |
B | ASN242 |
B | ALA245 |
B | ARG247 |
B | VAL281 |
B | ARG325 |
B | GLU328 |
B | NAP403 |
B | HOH565 |
B | HOH575 |
B | HOH616 |
B | HOH631 |
B | HOH653 |
B | HOH663 |
site_id | AC3 |
Number of Residues | 40 |
Details | binding site for residue NAP B 403 |
Chain | Residue |
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 | F7E402 |
B | EDO406 |
B | HOH543 |
B | HOH570 |
B | HOH575 |
B | HOH585 |
B | HOH586 |
B | HOH588 |
B | HOH590 |
B | HOH633 |
B | HOH676 |
B | HOH689 |
E | ARG56 |
E | SER57 |
E | SER58 |
E | HOH4225 |
site_id | AC4 |
Number of Residues | 4 |
Details | binding site for residue EDO B 404 |
Chain | Residue |
B | ARG176 |
B | PRO326 |
B | HOH618 |
C | GLU195 |
site_id | AC5 |
Number of Residues | 4 |
Details | binding site for residue EDO B 405 |
Chain | Residue |
B | ARG194 |
B | GLU195 |
B | EDO407 |
B | HOH508 |
site_id | AC6 |
Number of Residues | 7 |
Details | binding site for residue EDO B 406 |
Chain | Residue |
B | ARG55 |
B | ASN61 |
B | NAP403 |
E | ARG55 |
E | SER57 |
E | ASN61 |
E | NAP4002 |
site_id | AC7 |
Number of Residues | 7 |
Details | binding site for residue EDO B 407 |
Chain | Residue |
C | TYR174 |
B | TYR187 |
B | TRP188 |
B | ARG194 |
B | EDO405 |
B | HOH548 |
B | HOH650 |
site_id | AC8 |
Number of Residues | 27 |
Details | binding site for residue F7E C 2001 |
Chain | Residue |
C | SER112 |
C | HIS113 |
C | VAL114 |
C | THR155 |
C | SER156 |
C | TYR179 |
C | ASN208 |
C | ARG214 |
C | ASN217 |
C | PHE218 |
C | VAL219 |
C | LYS222 |
C | LEU240 |
C | GLY241 |
C | ASN242 |
C | ALA245 |
C | ARG247 |
C | VAL281 |
C | ARG325 |
C | GLU328 |
C | NAP2002 |
C | HOH2186 |
C | HOH2196 |
C | HOH2199 |
C | HOH2212 |
C | HOH2213 |
C | HOH2230 |
site_id | AC9 |
Number of Residues | 40 |
Details | binding site for residue NAP C 2002 |
Chain | Residue |
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 | F7E2001 |
C | HOH2135 |
C | HOH2164 |
C | HOH2171 |
C | HOH2175 |
C | HOH2212 |
C | HOH2217 |
C | HOH2226 |
C | HOH2233 |
C | HOH2236 |
C | HOH2249 |
C | HOH2257 |
C | HOH2268 |
D | ARG56 |
D | SER57 |
D | SER58 |
D | EDO3003 |
site_id | AD1 |
Number of Residues | 7 |
Details | binding site for residue EDO C 2003 |
Chain | Residue |
B | TYR174 |
C | TYR187 |
C | TRP188 |
C | ARG194 |
C | ASP270 |
C | HOH2110 |
C | HOH2146 |
site_id | AD2 |
Number of Residues | 3 |
Details | binding site for residue EDO C 2004 |
Chain | Residue |
C | ARG194 |
C | GLU195 |
C | HOH2107 |
site_id | AD3 |
Number of Residues | 29 |
Details | binding site for residue F7E D 3001 |
Chain | Residue |
D | SER112 |
D | HIS113 |
D | VAL114 |
D | THR155 |
D | SER156 |
D | TYR179 |
D | ASN208 |
D | ARG214 |
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 | NAP3002 |
D | HOH3110 |
D | HOH3132 |
D | HOH3161 |
D | HOH3194 |
D | HOH3218 |
D | HOH3226 |
D | HOH3227 |
site_id | AD4 |
Number of Residues | 40 |
Details | binding site for residue NAP D 3002 |
Chain | Residue |
C | ARG56 |
C | SER57 |
C | SER58 |
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 | F7E3001 |
D | EDO3003 |
D | HOH3114 |
D | HOH3120 |
D | HOH3132 |
D | HOH3164 |
D | HOH3186 |
D | HOH3189 |
D | HOH3191 |
D | HOH3198 |
D | HOH3200 |
D | HOH3204 |
D | HOH3219 |
D | HOH3232 |
site_id | AD5 |
Number of Residues | 8 |
Details | binding site for residue EDO D 3003 |
Chain | Residue |
C | ARG55 |
C | SER57 |
C | ASN61 |
C | NAP2002 |
D | ARG55 |
D | SER57 |
D | ASN61 |
D | NAP3002 |
site_id | AD6 |
Number of Residues | 6 |
Details | binding site for residue EDO D 3004 |
Chain | Residue |
D | TYR187 |
D | TRP188 |
D | ARG194 |
D | ASP270 |
D | HOH3169 |
D | HOH3197 |
site_id | AD7 |
Number of Residues | 4 |
Details | binding site for residue EDO D 3005 |
Chain | Residue |
D | TYR174 |
D | HOH3103 |
E | TYR187 |
E | TRP188 |
site_id | AD8 |
Number of Residues | 29 |
Details | binding site for residue F7E E 4001 |
Chain | Residue |
E | SER112 |
E | VAL114 |
E | THR155 |
E | SER156 |
E | GLU157 |
E | TYR179 |
E | ASN208 |
E | ARG214 |
E | ASN217 |
E | PHE218 |
E | VAL219 |
E | LYS222 |
E | LEU240 |
E | GLY241 |
E | ASN242 |
E | ALA245 |
E | ARG247 |
E | VAL281 |
E | TYR323 |
E | ARG325 |
E | GLU328 |
E | NAP4002 |
E | HOH4125 |
E | HOH4143 |
E | HOH4175 |
E | HOH4210 |
E | HOH4215 |
E | HOH4217 |
E | HOH4243 |
site_id | AD9 |
Number of Residues | 39 |
Details | binding site for residue NAP E 4002 |
Chain | Residue |
B | ARG56 |
B | SER57 |
B | SER58 |
B | EDO406 |
E | GLY30 |
E | THR32 |
E | GLY33 |
E | GLN34 |
E | ASP35 |
E | ARG55 |
E | ASP86 |
E | LEU87 |
E | LEU108 |
E | GLY109 |
E | ALA110 |
E | SER112 |
E | TYR123 |
E | VAL127 |
E | ALA153 |
E | SER154 |
E | THR155 |
E | TYR179 |
E | LYS183 |
E | LEU206 |
E | ASN208 |
E | HIS209 |
E | ARG214 |
E | F7E4001 |
E | HOH4143 |
E | HOH4145 |
E | HOH4152 |
E | HOH4168 |
E | HOH4179 |
E | HOH4185 |
E | HOH4187 |
E | HOH4197 |
E | HOH4239 |
E | HOH4251 |
E | HOH4262 |
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 |
B | 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 |
B | THR155 | |
C | THR155 | |
D | THR155 | |
E | THR155 |
site_id | SWS_FT_FI2 |
Number of Residues | 8 |
Details | ACT_SITE: Nucleophile => ECO:0000250 |
Chain | Residue | Details |
D | GLU157 | |
D | TYR179 | |
E | GLU157 | |
E | TYR179 | |
B | GLU157 | |
B | TYR179 | |
C | GLU157 | |
C | TYR179 |
site_id | SWS_FT_FI3 |
Number of Residues | 32 |
Details | BINDING: BINDING => ECO:0000269|Ref.9 |
Chain | Residue | Details |
C | GLY30 | |
C | ARG55 | |
C | ASP86 | |
C | LEU108 | |
C | TYR123 | |
C | LYS183 | |
C | HIS209 | |
C | ARG214 | |
D | GLY30 | |
D | ARG55 | |
D | ASP86 | |
D | LEU108 | |
D | TYR123 | |
D | LYS183 | |
D | HIS209 | |
D | ARG214 | |
E | GLY30 | |
E | ARG55 | |
E | ASP86 | |
E | LEU108 | |
E | TYR123 | |
E | LYS183 | |
E | HIS209 | |
E | ARG214 | |
B | GLY30 | |
B | ARG55 | |
B | ASP86 | |
B | LEU108 | |
B | TYR123 | |
B | LYS183 | |
B | HIS209 | |
B | ARG214 |
site_id | SWS_FT_FI4 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
B | TYR323 | |
C | TYR323 | |
D | TYR323 | |
E | TYR323 |