6GPK
Crystal structure of human GDP-D-mannose 4,6-dehydratase (E157Q) 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 |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 401 |
| Chain | Residue |
| A | PHE173 |
| A | LEU184 |
| A | TRP188 |
| A | EDO407 |
| A | HOH634 |
| D | PHE173 |
| D | TRP188 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 402 |
| Chain | Residue |
| A | ASN61 |
| A | NAP414 |
| B | ARG55 |
| B | ASN61 |
| B | NAP408 |
| A | ARG55 |
| A | SER57 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 403 |
| Chain | Residue |
| A | ARG282 |
| A | TRP298 |
| A | GLY300 |
| A | GLU305 |
| A | HOH506 |
| B | ARG367 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | ARG134 |
| A | HOH558 |
| A | HOH576 |
| C | THR88 |
| C | HOH527 |
| D | GLU122 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | TYR187 |
| A | TRP188 |
| A | ARG194 |
| A | HOH519 |
| A | HOH524 |
| A | HOH633 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | THR88 |
| A | HOH534 |
| A | HOH553 |
| B | GLU122 |
| B | HOH527 |
| C | ARG134 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | GLU169 |
| A | THR170 |
| A | THR171 |
| A | PHE173 |
| A | EDO401 |
| A | HOH542 |
| A | HOH653 |
| site_id | AC8 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | ARG176 |
| A | HOH682 |
| D | GLU195 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | PRO347 |
| A | ARG348 |
| A | VAL349 |
| A | HOH526 |
| A | HOH552 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 410 |
| Chain | Residue |
| A | HIS291 |
| A | HIS360 |
| A | HOH513 |
| site_id | AD2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 411 |
| Chain | Residue |
| A | ARG194 |
| A | GLU195 |
| A | HOH670 |
| site_id | AD3 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 412 |
| Chain | Residue |
| A | GLU164 |
| A | PRO172 |
| A | TYR231 |
| A | LEU232 |
| A | ARG367 |
| A | HOH679 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue EDO A 413 |
| Chain | Residue |
| A | PHE118 |
| A | ASP119 |
| A | LEU120 |
| A | ALA121 |
| A | GLU122 |
| A | HOH531 |
| B | ASP89 |
| B | THR91 |
| D | ASP137 |
| site_id | AD5 |
| Number of Residues | 39 |
| Details | binding site for residue NAP A 414 |
| Chain | Residue |
| A | HOH604 |
| A | HOH607 |
| A | HOH611 |
| A | HOH621 |
| A | HOH623 |
| A | HOH626 |
| A | HOH628 |
| A | HOH648 |
| A | HOH672 |
| A | HOH696 |
| B | ARG56 |
| B | SER57 |
| B | SER58 |
| B | HOH513 |
| 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 | TYR179 |
| A | LYS183 |
| A | LEU206 |
| A | ASN208 |
| A | HIS209 |
| A | ARG214 |
| A | EDO402 |
| A | GDD415 |
| A | HOH543 |
| site_id | AD6 |
| Number of Residues | 27 |
| Details | binding site for residue GDD A 415 |
| Chain | Residue |
| A | SER112 |
| A | VAL114 |
| A | THR155 |
| A | SER156 |
| A | GLN157 |
| A | TYR179 |
| A | ASN208 |
| A | ARG214 |
| A | ASN217 |
| A | VAL219 |
| A | LYS222 |
| A | LEU240 |
| A | GLY241 |
| A | ASN242 |
| A | ALA245 |
| A | ARG247 |
| A | VAL281 |
| A | ARG325 |
| A | GLU328 |
| A | LEU332 |
| A | NAP414 |
| A | HOH577 |
| A | HOH606 |
| A | HOH607 |
| A | HOH645 |
| A | HOH652 |
| A | HOH658 |
| site_id | AD7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 401 |
| Chain | Residue |
| B | ASP137 |
| B | TYR197 |
| B | HOH519 |
| B | HOH574 |
| C | PHE118 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 402 |
| Chain | Residue |
| A | GLU122 |
| B | THR88 |
| B | HOH520 |
| B | HOH533 |
| B | HOH541 |
| D | ARG134 |
| site_id | AD9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO B 403 |
| Chain | Residue |
| B | PHE173 |
| B | LEU184 |
| B | TRP188 |
| B | HOH538 |
| B | HOH589 |
| C | PHE173 |
| C | TRP188 |
| site_id | AE1 |
| Number of Residues | 6 |
| Details | binding site for residue EDO B 404 |
| Chain | Residue |
| B | ARG134 |
| B | HOH540 |
| C | GLU122 |
| C | HOH543 |
| D | THR88 |
| D | HOH513 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| B | ARG194 |
| B | GLU195 |
| B | EDO407 |
| B | HOH515 |
| site_id | AE3 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | LEU82 |
| B | HOH576 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | TYR187 |
| B | ARG194 |
| B | EDO405 |
| site_id | AE5 |
| Number of Residues | 38 |
| Details | binding site for residue NAP B 408 |
| Chain | Residue |
| A | ARG56 |
| A | SER57 |
| A | SER58 |
| A | EDO402 |
| A | HOH539 |
| 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 | TYR179 |
| B | LYS183 |
| B | LEU206 |
| B | ASN208 |
| B | HIS209 |
| B | ARG214 |
| B | GDD409 |
| B | HOH563 |
| B | HOH601 |
| B | HOH608 |
| B | HOH610 |
| B | HOH616 |
| B | HOH618 |
| B | HOH625 |
| B | HOH628 |
| B | HOH666 |
| B | HOH684 |
| site_id | AE6 |
| Number of Residues | 27 |
| Details | binding site for residue GDD B 409 |
| Chain | Residue |
| B | SER112 |
| B | VAL114 |
| B | THR155 |
| B | SER156 |
| B | GLN157 |
| B | TYR179 |
| B | ASN208 |
| B | ARG214 |
| B | ASN217 |
| B | VAL219 |
| B | LYS222 |
| B | LEU240 |
| B | GLY241 |
| B | ASN242 |
| B | ALA245 |
| B | ARG247 |
| B | VAL281 |
| B | ARG325 |
| B | GLU328 |
| B | LEU332 |
| B | NAP408 |
| B | HOH564 |
| B | HOH599 |
| B | HOH601 |
| B | HOH637 |
| B | HOH643 |
| B | HOH667 |
| site_id | AE7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 401 |
| Chain | Residue |
| C | TRP298 |
| C | GLU299 |
| C | GLY300 |
| C | GLU305 |
| C | GOL406 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO C 402 |
| Chain | Residue |
| A | ASN265 |
| A | LYS342 |
| A | HOH649 |
| A | HOH657 |
| C | GLN341 |
| site_id | AE9 |
| Number of Residues | 7 |
| Details | binding site for residue EDO C 403 |
| Chain | Residue |
| C | ARG55 |
| C | SER57 |
| C | ASN61 |
| C | NAP407 |
| D | ARG55 |
| D | ASN61 |
| D | NAP404 |
| site_id | AF1 |
| Number of Residues | 2 |
| Details | binding site for residue EDO C 404 |
| Chain | Residue |
| C | ARG194 |
| C | GLU195 |
| site_id | AF2 |
| Number of Residues | 4 |
| Details | binding site for residue EDO C 405 |
| Chain | Residue |
| C | TYR187 |
| C | TRP188 |
| C | ARG194 |
| C | HOH521 |
| site_id | AF3 |
| Number of Residues | 3 |
| Details | binding site for residue GOL C 406 |
| Chain | Residue |
| C | ARG282 |
| C | EDO401 |
| D | ARG367 |
| site_id | AF4 |
| Number of Residues | 39 |
| Details | binding site for residue NAP C 407 |
| 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 | EDO403 |
| C | GDD408 |
| C | HOH529 |
| C | HOH545 |
| C | HOH558 |
| C | HOH562 |
| C | HOH581 |
| C | HOH587 |
| C | HOH591 |
| C | HOH596 |
| C | HOH607 |
| C | HOH616 |
| C | HOH648 |
| D | ARG56 |
| D | SER57 |
| D | SER58 |
| site_id | AF5 |
| Number of Residues | 27 |
| Details | binding site for residue GDD C 408 |
| Chain | Residue |
| C | SER112 |
| C | THR155 |
| C | SER156 |
| C | GLN157 |
| C | TYR179 |
| C | ASN208 |
| C | ARG214 |
| C | ASN217 |
| C | VAL219 |
| C | LYS222 |
| C | LEU240 |
| C | GLY241 |
| C | ASN242 |
| C | ALA245 |
| C | ARG247 |
| C | VAL281 |
| C | TYR323 |
| C | ARG325 |
| C | GLU328 |
| C | LEU332 |
| C | NAP407 |
| C | HOH554 |
| C | HOH567 |
| C | HOH587 |
| C | HOH615 |
| C | HOH618 |
| C | HOH619 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue EDO D 401 |
| Chain | Residue |
| A | TYR231 |
| A | HIS291 |
| A | GLY293 |
| D | GLU164 |
| D | LYS168 |
| D | THR170 |
| site_id | AF7 |
| Number of Residues | 3 |
| Details | binding site for residue EDO D 402 |
| Chain | Residue |
| D | ARG194 |
| D | GLU195 |
| D | HOH514 |
| site_id | AF8 |
| Number of Residues | 4 |
| Details | binding site for residue EDO D 403 |
| Chain | Residue |
| D | TYR187 |
| D | TRP188 |
| D | ARG194 |
| D | HOH533 |
| site_id | AF9 |
| Number of Residues | 38 |
| Details | binding site for residue NAP D 404 |
| Chain | Residue |
| C | ARG56 |
| C | SER57 |
| C | SER58 |
| C | EDO403 |
| C | HOH605 |
| 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 | TYR179 |
| D | LYS183 |
| D | LEU206 |
| D | ASN208 |
| D | HIS209 |
| D | ARG214 |
| D | GDD405 |
| D | HOH525 |
| D | HOH528 |
| D | HOH540 |
| D | HOH554 |
| D | HOH570 |
| D | HOH581 |
| D | HOH582 |
| D | HOH586 |
| D | HOH603 |
| D | HOH619 |
| site_id | AG1 |
| Number of Residues | 27 |
| Details | binding site for residue GDD D 405 |
| Chain | Residue |
| D | SER112 |
| D | VAL114 |
| D | THR155 |
| D | SER156 |
| D | GLN157 |
| 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 | NAP404 |
| D | HOH525 |
| D | HOH543 |
| D | HOH565 |
| D | HOH590 |
| D | HOH591 |
| D | HOH608 |
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 |
