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 | 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 | GLN157 | |
A | TYR179 | |
B | GLN157 | |
B | TYR179 | |
C | GLN157 | |
C | TYR179 | |
D | GLN157 | |
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 |