6GPJ
Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4F-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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue CIT A 401 |
| Chain | Residue |
| A | ASN217 |
| A | LYS222 |
| A | TYR323 |
| A | HOH538 |
| A | HOH549 |
| A | HOH574 |
| B | TYR84 |
| site_id | AC2 |
| Number of Residues | 29 |
| Details | binding site for residue G4F A 402 |
| Chain | Residue |
| A | THR155 |
| A | SER156 |
| A | GLU157 |
| A | TYR179 |
| A | ASN208 |
| A | ARG214 |
| 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 | LEU332 |
| A | NAP403 |
| A | HOH549 |
| A | HOH558 |
| A | HOH577 |
| A | HOH590 |
| A | HOH597 |
| A | HOH638 |
| A | SER112 |
| A | VAL114 |
| site_id | AC3 |
| Number of Residues | 39 |
| Details | binding site for residue NAP A 403 |
| Chain | Residue |
| A | GLY30 |
| A | THR32 |
| A | GLY33 |
| A | GLN34 |
| A | ASP35 |
| A | ARG55 |
| A | ASP86 |
| A | LEU87 |
| A | LEU108 |
| A | GLY109 |
| A | ALA110 |
| A | SER112 |
| A | TYR123 |
| A | VAL127 |
| A | ALA153 |
| A | SER154 |
| A | THR155 |
| A | TYR179 |
| A | LYS183 |
| A | LEU206 |
| A | ASN208 |
| A | HIS209 |
| A | ARG214 |
| A | G4F402 |
| A | HOH540 |
| A | HOH552 |
| A | HOH577 |
| A | HOH584 |
| A | HOH585 |
| A | HOH596 |
| A | HOH598 |
| A | HOH601 |
| A | HOH605 |
| A | HOH624 |
| A | HOH631 |
| B | ARG56 |
| B | SER57 |
| B | SER58 |
| B | HOH503 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 401 |
| Chain | Residue |
| D | TYR187 |
| D | ASP270 |
| D | HOH541 |
| site_id | AC5 |
| Number of Residues | 27 |
| Details | binding site for residue G4F D 402 |
| Chain | Residue |
| D | HOH543 |
| D | HOH567 |
| D | HOH573 |
| D | HOH584 |
| D | HOH586 |
| D | HOH631 |
| D | SER112 |
| D | VAL114 |
| D | THR155 |
| D | SER156 |
| D | GLU157 |
| D | TYR179 |
| D | ASN208 |
| D | ARG214 |
| D | ASN217 |
| D | VAL219 |
| D | LYS222 |
| D | LEU240 |
| D | GLY241 |
| D | ASN242 |
| D | ALA245 |
| D | ARG247 |
| D | VAL281 |
| D | ARG325 |
| D | GLU328 |
| D | LEU332 |
| D | NAP403 |
| site_id | AC6 |
| Number of Residues | 39 |
| Details | binding site for residue NAP D 403 |
| Chain | Residue |
| C | ARG56 |
| C | SER57 |
| C | SER58 |
| C | HOH506 |
| C | HOH569 |
| 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 | G4F402 |
| D | HOH519 |
| D | HOH528 |
| D | HOH542 |
| D | HOH543 |
| D | HOH565 |
| D | HOH572 |
| D | HOH594 |
| D | HOH596 |
| D | HOH604 |
| D | HOH607 |
| site_id | AC7 |
| Number of Residues | 28 |
| Details | binding site for residue G4F C 401 |
| Chain | Residue |
| C | SER112 |
| C | VAL114 |
| C | THR155 |
| C | SER156 |
| C | GLU157 |
| 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 | LEU332 |
| C | NAP402 |
| C | HOH534 |
| C | HOH560 |
| C | HOH601 |
| C | HOH605 |
| C | HOH610 |
| C | HOH614 |
| site_id | AC8 |
| Number of Residues | 39 |
| Details | binding site for residue NAP C 402 |
| 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 | G4F401 |
| C | HOH509 |
| C | HOH522 |
| C | HOH559 |
| C | HOH560 |
| C | HOH575 |
| C | HOH586 |
| C | HOH590 |
| C | HOH592 |
| C | HOH596 |
| C | HOH597 |
| C | HOH599 |
| D | ARG56 |
| D | SER57 |
| D | SER58 |
| D | HOH559 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 401 |
| Chain | Residue |
| A | HOH520 |
| B | SER57 |
| B | SER58 |
| B | SER59 |
| B | ASN61 |
| B | HOH595 |
| B | HOH638 |
| B | HOH665 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue CIT B 402 |
| Chain | Residue |
| A | TYR84 |
| B | ASN217 |
| B | LYS222 |
| B | TYR323 |
| B | HOH576 |
| site_id | AD2 |
| Number of Residues | 28 |
| Details | binding site for residue G4F B 403 |
| Chain | Residue |
| B | SER112 |
| B | VAL114 |
| B | THR155 |
| B | SER156 |
| B | GLU157 |
| 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 | LEU332 |
| B | NAP404 |
| B | HOH530 |
| B | HOH561 |
| B | HOH564 |
| B | HOH576 |
| B | HOH581 |
| B | HOH629 |
| site_id | AD3 |
| Number of Residues | 39 |
| Details | binding site for residue NAP B 404 |
| Chain | Residue |
| A | ARG56 |
| A | SER57 |
| A | SER58 |
| A | HOH509 |
| 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 | G4F403 |
| B | HOH530 |
| B | HOH534 |
| B | HOH538 |
| B | HOH558 |
| B | HOH560 |
| B | HOH580 |
| B | HOH597 |
| B | HOH601 |
| B | HOH631 |
| B | HOH634 |
| B | HOH656 |
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 | |
| D | THR155 | |
| C | THR155 | |
| B | THR155 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 8 |
| Details | ACT_SITE: Nucleophile => ECO:0000250 |
| Chain | Residue | Details |
| A | GLU157 | |
| A | TYR179 | |
| D | GLU157 | |
| D | TYR179 | |
| C | GLU157 | |
| C | TYR179 | |
| B | GLU157 | |
| B | TYR179 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 32 |
| Details | BINDING: BINDING => ECO:0000269|Ref.9 |
| Chain | Residue | Details |
| A | GLY30 | |
| D | ARG55 | |
| D | ASP86 | |
| D | LEU108 | |
| D | TYR123 | |
| D | LYS183 | |
| D | HIS209 | |
| D | ARG214 | |
| C | GLY30 | |
| C | ARG55 | |
| C | ASP86 | |
| A | ARG55 | |
| C | LEU108 | |
| C | TYR123 | |
| C | LYS183 | |
| C | HIS209 | |
| C | ARG214 | |
| B | GLY30 | |
| B | ARG55 | |
| B | ASP86 | |
| B | LEU108 | |
| B | TYR123 | |
| A | ASP86 | |
| B | LYS183 | |
| B | HIS209 | |
| B | ARG214 | |
| A | LEU108 | |
| A | TYR123 | |
| A | LYS183 | |
| A | HIS209 | |
| A | ARG214 | |
| D | GLY30 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | TYR323 | |
| D | TYR323 | |
| C | TYR323 | |
| B | TYR323 |
