2JKV
Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0004616 | molecular_function | phosphogluconate dehydrogenase (decarboxylating) activity |
A | 0005634 | cellular_component | nucleus |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0006098 | biological_process | pentose-phosphate shunt |
A | 0009051 | biological_process | pentose-phosphate shunt, oxidative branch |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0019322 | biological_process | pentose biosynthetic process |
A | 0019521 | biological_process | D-gluconate metabolic process |
A | 0046177 | biological_process | D-gluconate catabolic process |
A | 0050661 | molecular_function | NADP binding |
A | 0070062 | cellular_component | extracellular exosome |
B | 0004616 | molecular_function | phosphogluconate dehydrogenase (decarboxylating) activity |
B | 0005634 | cellular_component | nucleus |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0006098 | biological_process | pentose-phosphate shunt |
B | 0009051 | biological_process | pentose-phosphate shunt, oxidative branch |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0019322 | biological_process | pentose biosynthetic process |
B | 0019521 | biological_process | D-gluconate metabolic process |
B | 0046177 | biological_process | D-gluconate catabolic process |
B | 0050661 | molecular_function | NADP binding |
B | 0070062 | cellular_component | extracellular exosome |
C | 0004616 | molecular_function | phosphogluconate dehydrogenase (decarboxylating) activity |
C | 0005634 | cellular_component | nucleus |
C | 0005737 | cellular_component | cytoplasm |
C | 0005829 | cellular_component | cytosol |
C | 0006098 | biological_process | pentose-phosphate shunt |
C | 0009051 | biological_process | pentose-phosphate shunt, oxidative branch |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0019322 | biological_process | pentose biosynthetic process |
C | 0019521 | biological_process | D-gluconate metabolic process |
C | 0046177 | biological_process | D-gluconate catabolic process |
C | 0050661 | molecular_function | NADP binding |
C | 0070062 | cellular_component | extracellular exosome |
D | 0004616 | molecular_function | phosphogluconate dehydrogenase (decarboxylating) activity |
D | 0005634 | cellular_component | nucleus |
D | 0005737 | cellular_component | cytoplasm |
D | 0005829 | cellular_component | cytosol |
D | 0006098 | biological_process | pentose-phosphate shunt |
D | 0009051 | biological_process | pentose-phosphate shunt, oxidative branch |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0019322 | biological_process | pentose biosynthetic process |
D | 0019521 | biological_process | D-gluconate metabolic process |
D | 0046177 | biological_process | D-gluconate catabolic process |
D | 0050661 | molecular_function | NADP binding |
D | 0070062 | cellular_component | extracellular exosome |
E | 0004616 | molecular_function | phosphogluconate dehydrogenase (decarboxylating) activity |
E | 0005634 | cellular_component | nucleus |
E | 0005737 | cellular_component | cytoplasm |
E | 0005829 | cellular_component | cytosol |
E | 0006098 | biological_process | pentose-phosphate shunt |
E | 0009051 | biological_process | pentose-phosphate shunt, oxidative branch |
E | 0016491 | molecular_function | oxidoreductase activity |
E | 0019322 | biological_process | pentose biosynthetic process |
E | 0019521 | biological_process | D-gluconate metabolic process |
E | 0046177 | biological_process | D-gluconate catabolic process |
E | 0050661 | molecular_function | NADP binding |
E | 0070062 | cellular_component | extracellular exosome |
F | 0004616 | molecular_function | phosphogluconate dehydrogenase (decarboxylating) activity |
F | 0005634 | cellular_component | nucleus |
F | 0005737 | cellular_component | cytoplasm |
F | 0005829 | cellular_component | cytosol |
F | 0006098 | biological_process | pentose-phosphate shunt |
F | 0009051 | biological_process | pentose-phosphate shunt, oxidative branch |
F | 0016491 | molecular_function | oxidoreductase activity |
F | 0019322 | biological_process | pentose biosynthetic process |
F | 0019521 | biological_process | D-gluconate metabolic process |
F | 0046177 | biological_process | D-gluconate catabolic process |
F | 0050661 | molecular_function | NADP binding |
F | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 34 |
Details | BINDING SITE FOR RESIDUE NAP A 500 |
Chain | Residue |
A | GLY451 |
A | HOH2256 |
A | HOH2257 |
A | HOH2258 |
B | GLY10 |
B | LEU11 |
B | ALA12 |
B | VAL13 |
B | MET14 |
B | ASN33 |
B | ARG34 |
A | HIS453 |
B | THR35 |
B | LYS38 |
B | LEU74 |
B | VAL75 |
B | LYS76 |
B | ALA77 |
B | ALA80 |
B | PHE84 |
B | GLY102 |
B | ASN103 |
A | SER478 |
B | VAL128 |
B | GLY131 |
B | CL1484 |
B | HOH2046 |
B | HOH2049 |
A | SER479 |
A | TYR481 |
A | HOH2252 |
A | HOH2253 |
A | HOH2254 |
A | HOH2255 |
site_id | AC2 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL A 1484 |
Chain | Residue |
A | ASN103 |
A | LYS184 |
A | ASN188 |
B | NAP500 |
site_id | AC3 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE SO4 A 1485 |
Chain | Residue |
A | TYR192 |
A | GLN260 |
A | LYS261 |
A | ARG288 |
A | HOH2160 |
A | HOH2259 |
A | HOH2260 |
A | HOH2261 |
B | ARG447 |
B | HIS453 |
site_id | AC4 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 A 1486 |
Chain | Residue |
A | LYS248 |
A | HIS249 |
A | HOH2262 |
A | HOH2263 |
site_id | AC5 |
Number of Residues | 30 |
Details | BINDING SITE FOR RESIDUE NAP B 500 |
Chain | Residue |
A | GLY10 |
A | LEU11 |
A | ALA12 |
A | VAL13 |
A | MET14 |
A | ASN33 |
A | ARG34 |
A | THR35 |
A | LYS38 |
A | LEU74 |
A | VAL75 |
A | LYS76 |
A | ALA77 |
A | ALA80 |
A | PHE84 |
A | GLY102 |
A | ASN103 |
A | VAL128 |
A | GLY131 |
A | CL1484 |
A | HOH2014 |
A | HOH2039 |
B | GLY451 |
B | SER478 |
B | SER479 |
B | TYR481 |
B | HOH2262 |
B | HOH2263 |
B | HOH2264 |
B | HOH2265 |
site_id | AC6 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL B 1484 |
Chain | Residue |
A | NAP500 |
B | ASN103 |
B | LYS184 |
B | ASN188 |
site_id | AC7 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL B 1485 |
Chain | Residue |
B | TRP150 |
B | LYS154 |
site_id | AC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 B 1486 |
Chain | Residue |
A | ARG447 |
B | TYR192 |
B | GLN260 |
B | LYS261 |
B | ARG288 |
B | HOH2165 |
B | HOH2266 |
B | HOH2267 |
site_id | AC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE SO4 B 1487 |
Chain | Residue |
B | HOH2269 |
B | LYS248 |
B | HIS249 |
B | HOH2158 |
site_id | BC1 |
Number of Residues | 32 |
Details | BINDING SITE FOR RESIDUE NAP C 500 |
Chain | Residue |
C | GLY451 |
C | HIS453 |
C | SER478 |
C | SER479 |
C | TYR481 |
C | HOH2191 |
C | HOH2192 |
C | HOH2193 |
C | HOH2194 |
D | GLY10 |
D | LEU11 |
D | ALA12 |
D | VAL13 |
D | MET14 |
D | ASN33 |
D | ARG34 |
D | THR35 |
D | LYS38 |
D | LEU74 |
D | VAL75 |
D | LYS76 |
D | ALA77 |
D | ALA80 |
D | PHE84 |
D | GLY102 |
D | ASN103 |
D | VAL128 |
D | GLY131 |
D | CL1486 |
D | HOH2053 |
D | HOH2054 |
D | HOH2133 |
site_id | BC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 C 1484 |
Chain | Residue |
C | TYR192 |
C | GLN260 |
C | LYS261 |
C | ARG288 |
C | HOH2106 |
C | HOH2127 |
C | HOH2195 |
D | ARG447 |
site_id | BC3 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE SO4 C 1485 |
Chain | Residue |
C | LYS248 |
C | HIS249 |
site_id | BC4 |
Number of Residues | 30 |
Details | BINDING SITE FOR RESIDUE NAP D 500 |
Chain | Residue |
C | GLY10 |
C | LEU11 |
C | ALA12 |
C | VAL13 |
C | MET14 |
C | ASN33 |
C | ARG34 |
C | THR35 |
C | LYS38 |
C | LEU74 |
C | VAL75 |
C | LYS76 |
C | ALA77 |
C | ALA80 |
C | PHE84 |
C | GLY102 |
C | ASN103 |
C | VAL128 |
C | GLY131 |
C | HOH2011 |
C | HOH2032 |
D | GLY451 |
D | HIS453 |
D | SER478 |
D | SER479 |
D | TYR481 |
D | HOH2184 |
D | HOH2188 |
D | HOH2189 |
D | HOH2190 |
site_id | BC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SO4 D 1484 |
Chain | Residue |
C | ARG447 |
C | HIS453 |
D | TYR192 |
D | LYS261 |
D | ARG288 |
D | HOH2113 |
D | HOH2134 |
D | HOH2191 |
site_id | BC6 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 D 1485 |
Chain | Residue |
D | LYS248 |
D | HIS249 |
D | HOH2130 |
site_id | BC7 |
Number of Residues | 33 |
Details | BINDING SITE FOR RESIDUE NAP E 500 |
Chain | Residue |
E | GLY451 |
E | HIS453 |
E | SER478 |
E | SER479 |
E | TYR481 |
E | HOH2226 |
E | HOH2232 |
E | HOH2233 |
E | HOH2234 |
E | HOH2235 |
F | GLY10 |
F | LEU11 |
F | ALA12 |
F | VAL13 |
F | MET14 |
F | ASN33 |
F | ARG34 |
F | THR35 |
F | LYS38 |
F | LEU74 |
F | VAL75 |
F | LYS76 |
F | ALA77 |
F | ALA80 |
F | PHE84 |
F | GLY102 |
F | ASN103 |
F | VAL128 |
F | GLY131 |
F | CL1473 |
F | HOH2050 |
F | HOH2054 |
F | HOH2159 |
site_id | BC8 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 E 1484 |
Chain | Residue |
E | LYS248 |
E | HIS249 |
E | HOH2237 |
site_id | BC9 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE SO4 E 1485 |
Chain | Residue |
E | TYR192 |
E | LYS261 |
E | ARG288 |
E | HOH2238 |
F | ARG447 |
site_id | CC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL F 1473 |
Chain | Residue |
E | NAP500 |
F | ASN103 |
F | LYS184 |
F | ASN188 |
F | HOH2247 |
site_id | CC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SO4 F 1474 |
Chain | Residue |
E | ARG447 |
E | HIS453 |
F | TYR192 |
F | GLN260 |
F | LYS261 |
F | ARG288 |
F | HOH2160 |
F | HOH2247 |
F | HOH2248 |
site_id | CC3 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE SO4 F 1475 |
Chain | Residue |
F | LYS248 |
F | HIS249 |
F | HOH2249 |
site_id | CC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL F 1476 |
Chain | Residue |
F | HOH2106 |
F | HOH2110 |
F | HOH2118 |
site_id | CC5 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE CL A 1488 |
Chain | Residue |
A | LYS303 |
site_id | CC6 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE CL E 1486 |
Chain | Residue |
E | TRP150 |
site_id | CC7 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CL A 1487 |
Chain | Residue |
A | TRP150 |
A | LYS154 |
A | ASP172 |
A | HOH2096 |
site_id | CC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE CL B 1488 |
Chain | Residue |
B | LYS303 |
B | HOH2174 |
site_id | CC9 |
Number of Residues | 1 |
Details | BINDING SITE FOR RESIDUE CL E 1488 |
Chain | Residue |
F | LYS396 |
site_id | DC1 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CL D 1486 |
Chain | Residue |
C | NAP500 |
D | SER129 |
D | LYS184 |
D | ILE367 |
D | HOH2112 |
Functional Information from PROSITE/UniProt
site_id | PS00461 |
Number of Residues | 13 |
Details | 6PGD 6-phosphogluconate dehydrogenase signature. IrDsaGQKGTGkW |
Chain | Residue | Details |
A | ILE254-TRP266 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 6 |
Details | ACT_SITE: Proton acceptor => ECO:0000250 |
Chain | Residue | Details |
A | LYS184 | |
B | LYS184 | |
C | LYS184 | |
D | LYS184 | |
E | LYS184 | |
F | LYS184 |
site_id | SWS_FT_FI2 |
Number of Residues | 6 |
Details | ACT_SITE: Proton donor => ECO:0000250 |
Chain | Residue | Details |
A | GLU191 | |
B | GLU191 | |
C | GLU191 | |
D | GLU191 | |
E | GLU191 | |
F | GLU191 |
site_id | SWS_FT_FI3 |
Number of Residues | 18 |
Details | BINDING: in other chain => ECO:0000269|Ref.9 |
Chain | Residue | Details |
A | GLY10 | |
D | GLY10 | |
D | ASN33 | |
D | VAL75 | |
E | GLY10 | |
E | ASN33 | |
E | VAL75 | |
F | GLY10 | |
F | ASN33 | |
F | VAL75 | |
A | ASN33 | |
A | VAL75 | |
B | GLY10 | |
B | ASN33 | |
B | VAL75 | |
C | GLY10 | |
C | ASN33 | |
C | VAL75 |
site_id | SWS_FT_FI4 |
Number of Residues | 36 |
Details | BINDING: in other chain => ECO:0000250 |
Chain | Residue | Details |
A | ASN103 | |
B | TYR192 | |
B | LYS261 | |
B | ARG288 | |
C | ASN103 | |
C | SER129 | |
C | HIS187 | |
C | TYR192 | |
C | LYS261 | |
C | ARG288 | |
D | ASN103 | |
A | SER129 | |
D | SER129 | |
D | HIS187 | |
D | TYR192 | |
D | LYS261 | |
D | ARG288 | |
E | ASN103 | |
E | SER129 | |
E | HIS187 | |
E | TYR192 | |
E | LYS261 | |
A | HIS187 | |
E | ARG288 | |
F | ASN103 | |
F | SER129 | |
F | HIS187 | |
F | TYR192 | |
F | LYS261 | |
F | ARG288 | |
A | TYR192 | |
A | LYS261 | |
A | ARG288 | |
B | ASN103 | |
B | SER129 | |
B | HIS187 |
site_id | SWS_FT_FI5 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
A | ARG447 | |
E | HIS453 | |
F | ARG447 | |
F | HIS453 | |
A | HIS453 | |
B | ARG447 | |
B | HIS453 | |
C | ARG447 | |
C | HIS453 | |
D | ARG447 | |
D | HIS453 | |
E | ARG447 |
site_id | SWS_FT_FI6 |
Number of Residues | 6 |
Details | BINDING: BINDING => ECO:0000269|Ref.9 |
Chain | Residue | Details |
A | SER478 | |
B | SER478 | |
C | SER478 | |
D | SER478 | |
E | SER478 | |
F | SER478 |
site_id | SWS_FT_FI7 |
Number of Residues | 6 |
Details | MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:Q9DCD0 |
Chain | Residue | Details |
A | LYS38 | |
B | LYS38 | |
C | LYS38 | |
D | LYS38 | |
E | LYS38 | |
F | LYS38 |
site_id | SWS_FT_FI8 |
Number of Residues | 12 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:Q9DCD0 |
Chain | Residue | Details |
A | SER57 | |
E | SER129 | |
F | SER57 | |
F | SER129 | |
A | SER129 | |
B | SER57 | |
B | SER129 | |
C | SER57 | |
C | SER129 | |
D | SER57 | |
D | SER129 | |
E | SER57 |
site_id | SWS_FT_FI9 |
Number of Residues | 12 |
Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
Chain | Residue | Details |
A | LYS59 | |
E | LYS309 | |
F | LYS59 | |
F | LYS309 | |
A | LYS309 | |
B | LYS59 | |
B | LYS309 | |
C | LYS59 | |
C | LYS309 | |
D | LYS59 | |
D | LYS309 | |
E | LYS59 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 2pgd |
Chain | Residue | Details |
A | GLY131 | |
A | GLU191 | |
A | LYS184 | |
A | ASN188 |
site_id | CSA2 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 2pgd |
Chain | Residue | Details |
B | GLY131 | |
B | GLU191 | |
B | LYS184 | |
B | ASN188 |
site_id | CSA3 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 2pgd |
Chain | Residue | Details |
C | GLY131 | |
C | GLU191 | |
C | LYS184 | |
C | ASN188 |
site_id | CSA4 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 2pgd |
Chain | Residue | Details |
D | GLY131 | |
D | GLU191 | |
D | LYS184 | |
D | ASN188 |
site_id | CSA5 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 2pgd |
Chain | Residue | Details |
E | GLY131 | |
E | GLU191 | |
E | LYS184 | |
E | ASN188 |
site_id | CSA6 |
Number of Residues | 4 |
Details | Annotated By Reference To The Literature 2pgd |
Chain | Residue | Details |
F | GLY131 | |
F | GLU191 | |
F | LYS184 | |
F | ASN188 |