6Q94
Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man
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 |
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 |
F | 0005515 | molecular_function | protein binding |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
F | 0007219 | biological_process | Notch signaling pathway |
F | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
F | 0016829 | molecular_function | lyase activity |
F | 0019673 | biological_process | GDP-mannose metabolic process |
F | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
F | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
F | 0042802 | molecular_function | identical protein binding |
F | 0070062 | cellular_component | extracellular exosome |
F | 0070401 | molecular_function | NADP+ binding |
G | 0005515 | molecular_function | protein binding |
G | 0005737 | cellular_component | cytoplasm |
G | 0005829 | cellular_component | cytosol |
G | 0007219 | biological_process | Notch signaling pathway |
G | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
G | 0016829 | molecular_function | lyase activity |
G | 0019673 | biological_process | GDP-mannose metabolic process |
G | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
G | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
G | 0042802 | molecular_function | identical protein binding |
G | 0070062 | cellular_component | extracellular exosome |
G | 0070401 | molecular_function | NADP+ binding |
H | 0005515 | molecular_function | protein binding |
H | 0005737 | cellular_component | cytoplasm |
H | 0005829 | cellular_component | cytosol |
H | 0007219 | biological_process | Notch signaling pathway |
H | 0008446 | molecular_function | GDP-mannose 4,6-dehydratase activity |
H | 0016829 | molecular_function | lyase activity |
H | 0019673 | biological_process | GDP-mannose metabolic process |
H | 0042350 | biological_process | GDP-L-fucose biosynthetic process |
H | 0042351 | biological_process | 'de novo' GDP-L-fucose biosynthetic process |
H | 0042802 | molecular_function | identical protein binding |
H | 0070062 | cellular_component | extracellular exosome |
H | 0070401 | molecular_function | NADP+ binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 22 |
Details | binding site for residue NAP B 401 |
Chain | Residue |
A | ARG56 |
B | ASN61 |
B | ASP86 |
B | LEU87 |
B | LEU108 |
B | GLY109 |
B | ALA110 |
B | SER112 |
B | TYR123 |
B | ALA153 |
B | TYR179 |
A | SER57 |
B | LYS183 |
B | ARG214 |
B | GDD402 |
A | SER58 |
B | GLY30 |
B | THR32 |
B | GLY33 |
B | GLN34 |
B | ASP35 |
B | ARG55 |
site_id | AC2 |
Number of Residues | 20 |
Details | binding site for residue GDD B 402 |
Chain | Residue |
B | SER112 |
B | HIS113 |
B | VAL114 |
B | THR155 |
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 | NAP401 |
site_id | AC3 |
Number of Residues | 22 |
Details | binding site for residue NAP A 401 |
Chain | Residue |
A | GLY30 |
A | THR32 |
A | GLY33 |
A | GLN34 |
A | ASP35 |
A | ARG55 |
A | ASN61 |
A | ASP86 |
A | LEU87 |
A | LEU108 |
A | GLY109 |
A | ALA110 |
A | SER112 |
A | TYR123 |
A | VAL127 |
A | ALA153 |
A | TYR179 |
A | LYS183 |
A | GDD402 |
B | ARG56 |
B | SER57 |
B | SER58 |
site_id | AC4 |
Number of Residues | 21 |
Details | binding site for residue GDD A 402 |
Chain | Residue |
A | SER112 |
A | THR155 |
A | ASP156 |
A | GLU157 |
A | TYR179 |
A | PHE207 |
A | ASN208 |
A | ARG214 |
A | ASN217 |
A | PHE218 |
A | VAL219 |
A | LYS222 |
A | LEU240 |
A | GLY241 |
A | ASN242 |
A | ALA245 |
A | ARG247 |
A | TYR323 |
A | ARG325 |
A | GLU328 |
A | NAP401 |
site_id | AC5 |
Number of Residues | 20 |
Details | binding site for residue NAP C 401 |
Chain | Residue |
C | ALA153 |
C | TYR179 |
C | LYS183 |
C | GDD402 |
E | ARG56 |
E | 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 |
site_id | AC6 |
Number of Residues | 22 |
Details | binding site for residue GDD C 402 |
Chain | Residue |
C | SER112 |
C | VAL114 |
C | THR155 |
C | ASP156 |
C | GLU157 |
C | TYR179 |
C | LEU206 |
C | PHE207 |
C | ASN208 |
C | ARG214 |
C | ASN217 |
C | PHE218 |
C | VAL219 |
C | LYS222 |
C | GLY241 |
C | ASN242 |
C | ALA245 |
C | ARG247 |
C | VAL281 |
C | ARG325 |
C | GLU328 |
C | NAP401 |
site_id | AC7 |
Number of Residues | 23 |
Details | binding site for residue NAP D 401 |
Chain | Residue |
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 | ALA153 |
D | THR155 |
D | TYR179 |
D | LYS183 |
D | ARG214 |
D | GDD402 |
F | ARG56 |
F | SER57 |
F | SER58 |
site_id | AC8 |
Number of Residues | 22 |
Details | binding site for residue GDD D 402 |
Chain | Residue |
D | SER112 |
D | VAL114 |
D | THR155 |
D | ASP156 |
D | GLU157 |
D | TYR179 |
D | PHE207 |
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 | ARG325 |
D | GLU328 |
D | NAP401 |
site_id | AC9 |
Number of Residues | 3 |
Details | binding site for residue EDO D 403 |
Chain | Residue |
D | TYR84 |
F | ASN217 |
F | TYR323 |
site_id | AD1 |
Number of Residues | 1 |
Details | binding site for residue EDO D 404 |
Chain | Residue |
D | ASN217 |
site_id | AD2 |
Number of Residues | 21 |
Details | binding site for residue NAP E 401 |
Chain | Residue |
C | ARG56 |
C | SER57 |
C | SER58 |
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 | TYR179 |
E | LYS183 |
E | GDD402 |
site_id | AD3 |
Number of Residues | 21 |
Details | binding site for residue GDD E 402 |
Chain | Residue |
E | SER112 |
E | VAL114 |
E | THR155 |
E | ASP156 |
E | TYR179 |
E | PHE207 |
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 | ARG325 |
E | GLU328 |
E | NAP401 |
site_id | AD4 |
Number of Residues | 21 |
Details | binding site for residue GDD F 401 |
Chain | Residue |
F | SER112 |
F | VAL114 |
F | THR155 |
F | ASP156 |
F | TYR179 |
F | LEU206 |
F | PHE207 |
F | ASN208 |
F | ARG214 |
F | ASN217 |
F | PHE218 |
F | VAL219 |
F | LYS222 |
F | GLY241 |
F | ASN242 |
F | ALA245 |
F | ARG247 |
F | VAL281 |
F | ARG325 |
F | GLU328 |
F | NAP402 |
site_id | AD5 |
Number of Residues | 22 |
Details | binding site for residue NAP F 402 |
Chain | Residue |
D | ARG56 |
D | SER57 |
D | SER58 |
F | GLY30 |
F | THR32 |
F | GLY33 |
F | GLN34 |
F | ASP35 |
F | ARG55 |
F | ASN61 |
F | ASP86 |
F | LEU87 |
F | LEU108 |
F | GLY109 |
F | ALA110 |
F | SER112 |
F | TYR123 |
F | VAL127 |
F | ALA153 |
F | TYR179 |
F | LYS183 |
F | GDD401 |
site_id | AD6 |
Number of Residues | 22 |
Details | binding site for residue NAP G 401 |
Chain | Residue |
G | GLY30 |
G | THR32 |
G | GLY33 |
G | GLN34 |
G | ASP35 |
G | ARG55 |
G | ASN61 |
G | ASP86 |
G | LEU87 |
G | LEU108 |
G | GLY109 |
G | ALA110 |
G | SER112 |
G | TYR123 |
G | VAL127 |
G | ALA153 |
G | TYR179 |
G | LYS183 |
G | GDD402 |
H | ARG56 |
H | SER57 |
H | SER58 |
site_id | AD7 |
Number of Residues | 21 |
Details | binding site for residue GDD G 402 |
Chain | Residue |
G | SER112 |
G | HIS113 |
G | VAL114 |
G | THR155 |
G | ASP156 |
G | TYR179 |
G | PHE207 |
G | ASN208 |
G | ARG214 |
G | ASN217 |
G | PHE218 |
G | VAL219 |
G | LYS222 |
G | LEU240 |
G | GLY241 |
G | ASN242 |
G | ALA245 |
G | ARG247 |
G | ARG325 |
G | GLU328 |
G | NAP401 |
site_id | AD8 |
Number of Residues | 2 |
Details | binding site for residue EDO G 403 |
Chain | Residue |
G | PHE60 |
G | HIS75 |
site_id | AD9 |
Number of Residues | 20 |
Details | binding site for residue NAP H 401 |
Chain | Residue |
G | ARG56 |
G | SER58 |
H | GLY30 |
H | THR32 |
H | GLY33 |
H | GLN34 |
H | ASP35 |
H | ARG55 |
H | ASP86 |
H | LEU87 |
H | LEU108 |
H | GLY109 |
H | ALA110 |
H | SER112 |
H | TYR123 |
H | VAL127 |
H | THR155 |
H | TYR179 |
H | LYS183 |
H | GDD402 |
site_id | AE1 |
Number of Residues | 20 |
Details | binding site for residue GDD H 402 |
Chain | Residue |
H | SER112 |
H | VAL114 |
H | THR155 |
H | ASP156 |
H | TYR179 |
H | ASN208 |
H | ARG214 |
H | ASN217 |
H | PHE218 |
H | VAL219 |
H | LYS222 |
H | LEU240 |
H | GLY241 |
H | ASN242 |
H | ALA245 |
H | ARG247 |
H | TYR323 |
H | ARG325 |
H | GLU328 |
H | NAP401 |
site_id | AE2 |
Number of Residues | 1 |
Details | binding site for residue EDO H 403 |
Chain | Residue |
H | TYR323 |
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 | 8 |
Details | ACT_SITE: ACT_SITE => ECO:0000250 |
Chain | Residue | Details |
B | THR155 | |
A | THR155 | |
C | THR155 | |
D | THR155 | |
E | THR155 | |
F | THR155 | |
G | THR155 | |
H | THR155 |
site_id | SWS_FT_FI2 |
Number of Residues | 16 |
Details | ACT_SITE: Nucleophile => ECO:0000250 |
Chain | Residue | Details |
B | GLU157 | |
E | TYR179 | |
F | GLU157 | |
F | TYR179 | |
G | GLU157 | |
G | TYR179 | |
H | GLU157 | |
H | TYR179 | |
B | TYR179 | |
A | GLU157 | |
A | TYR179 | |
C | GLU157 | |
C | TYR179 | |
D | GLU157 | |
D | TYR179 | |
E | GLU157 |
site_id | SWS_FT_FI3 |
Number of Residues | 64 |
Details | BINDING: BINDING => ECO:0000269|Ref.9 |
Chain | Residue | Details |
B | GLY30 | |
A | ARG55 | |
A | ASP86 | |
A | LEU108 | |
A | TYR123 | |
A | LYS183 | |
A | HIS209 | |
A | ARG214 | |
C | GLY30 | |
C | ARG55 | |
C | ASP86 | |
B | ARG55 | |
C | LEU108 | |
C | TYR123 | |
C | LYS183 | |
C | HIS209 | |
C | ARG214 | |
D | GLY30 | |
D | ARG55 | |
D | ASP86 | |
D | LEU108 | |
D | TYR123 | |
B | ASP86 | |
D | LYS183 | |
D | HIS209 | |
D | ARG214 | |
E | GLY30 | |
E | ARG55 | |
E | ASP86 | |
E | LEU108 | |
E | TYR123 | |
E | LYS183 | |
E | HIS209 | |
B | LEU108 | |
E | ARG214 | |
F | GLY30 | |
F | ARG55 | |
F | ASP86 | |
F | LEU108 | |
F | TYR123 | |
F | LYS183 | |
F | HIS209 | |
F | ARG214 | |
G | GLY30 | |
B | TYR123 | |
G | ARG55 | |
G | ASP86 | |
G | LEU108 | |
G | TYR123 | |
G | LYS183 | |
G | HIS209 | |
G | ARG214 | |
H | GLY30 | |
H | ARG55 | |
H | ASP86 | |
B | LYS183 | |
H | LEU108 | |
H | TYR123 | |
H | LYS183 | |
H | HIS209 | |
H | ARG214 | |
B | HIS209 | |
B | ARG214 | |
A | GLY30 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:23186163 |
Chain | Residue | Details |
B | TYR323 | |
A | TYR323 | |
C | TYR323 | |
D | TYR323 | |
E | TYR323 | |
F | TYR323 | |
G | TYR323 | |
H | TYR323 |