3ITK
Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, apo form.
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0001702 | biological_process | gastrulation with mouth forming second |
| A | 0003979 | molecular_function | UDP-glucose 6-dehydrogenase activity |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005829 | cellular_component | cytosol |
| A | 0006024 | biological_process | glycosaminoglycan biosynthetic process |
| A | 0006065 | biological_process | UDP-glucuronate biosynthetic process |
| A | 0015012 | biological_process | heparan sulfate proteoglycan biosynthetic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| A | 0030206 | biological_process | chondroitin sulfate biosynthetic process |
| A | 0034214 | biological_process | protein hexamerization |
| A | 0042802 | molecular_function | identical protein binding |
| A | 0048666 | biological_process | neuron development |
| A | 0051287 | molecular_function | NAD binding |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0001702 | biological_process | gastrulation with mouth forming second |
| B | 0003979 | molecular_function | UDP-glucose 6-dehydrogenase activity |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005829 | cellular_component | cytosol |
| B | 0006024 | biological_process | glycosaminoglycan biosynthetic process |
| B | 0006065 | biological_process | UDP-glucuronate biosynthetic process |
| B | 0015012 | biological_process | heparan sulfate proteoglycan biosynthetic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| B | 0030206 | biological_process | chondroitin sulfate biosynthetic process |
| B | 0034214 | biological_process | protein hexamerization |
| B | 0042802 | molecular_function | identical protein binding |
| B | 0048666 | biological_process | neuron development |
| B | 0051287 | molecular_function | NAD binding |
| B | 0070062 | cellular_component | extracellular exosome |
| C | 0001702 | biological_process | gastrulation with mouth forming second |
| C | 0003979 | molecular_function | UDP-glucose 6-dehydrogenase activity |
| C | 0005634 | cellular_component | nucleus |
| C | 0005654 | cellular_component | nucleoplasm |
| C | 0005829 | cellular_component | cytosol |
| C | 0006024 | biological_process | glycosaminoglycan biosynthetic process |
| C | 0006065 | biological_process | UDP-glucuronate biosynthetic process |
| C | 0015012 | biological_process | heparan sulfate proteoglycan biosynthetic process |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| C | 0030206 | biological_process | chondroitin sulfate biosynthetic process |
| C | 0034214 | biological_process | protein hexamerization |
| C | 0042802 | molecular_function | identical protein binding |
| C | 0048666 | biological_process | neuron development |
| C | 0051287 | molecular_function | NAD binding |
| C | 0070062 | cellular_component | extracellular exosome |
| D | 0001702 | biological_process | gastrulation with mouth forming second |
| D | 0003979 | molecular_function | UDP-glucose 6-dehydrogenase activity |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005829 | cellular_component | cytosol |
| D | 0006024 | biological_process | glycosaminoglycan biosynthetic process |
| D | 0006065 | biological_process | UDP-glucuronate biosynthetic process |
| D | 0015012 | biological_process | heparan sulfate proteoglycan biosynthetic process |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| D | 0030206 | biological_process | chondroitin sulfate biosynthetic process |
| D | 0034214 | biological_process | protein hexamerization |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0048666 | biological_process | neuron development |
| D | 0051287 | molecular_function | NAD binding |
| D | 0070062 | cellular_component | extracellular exosome |
| E | 0001702 | biological_process | gastrulation with mouth forming second |
| E | 0003979 | molecular_function | UDP-glucose 6-dehydrogenase activity |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005829 | cellular_component | cytosol |
| E | 0006024 | biological_process | glycosaminoglycan biosynthetic process |
| E | 0006065 | biological_process | UDP-glucuronate biosynthetic process |
| E | 0015012 | biological_process | heparan sulfate proteoglycan biosynthetic process |
| E | 0016491 | molecular_function | oxidoreductase activity |
| E | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| E | 0030206 | biological_process | chondroitin sulfate biosynthetic process |
| E | 0034214 | biological_process | protein hexamerization |
| E | 0042802 | molecular_function | identical protein binding |
| E | 0048666 | biological_process | neuron development |
| E | 0051287 | molecular_function | NAD binding |
| E | 0070062 | cellular_component | extracellular exosome |
| F | 0001702 | biological_process | gastrulation with mouth forming second |
| F | 0003979 | molecular_function | UDP-glucose 6-dehydrogenase activity |
| F | 0005634 | cellular_component | nucleus |
| F | 0005654 | cellular_component | nucleoplasm |
| F | 0005829 | cellular_component | cytosol |
| F | 0006024 | biological_process | glycosaminoglycan biosynthetic process |
| F | 0006065 | biological_process | UDP-glucuronate biosynthetic process |
| F | 0015012 | biological_process | heparan sulfate proteoglycan biosynthetic process |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0016616 | molecular_function | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor |
| F | 0030206 | biological_process | chondroitin sulfate biosynthetic process |
| F | 0034214 | biological_process | protein hexamerization |
| F | 0042802 | molecular_function | identical protein binding |
| F | 0048666 | biological_process | neuron development |
| F | 0051287 | molecular_function | NAD binding |
| F | 0070062 | cellular_component | extracellular exosome |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PG4 A 467 |
| Chain | Residue |
| A | PHE265 |
| A | PHE272 |
| A | GLY273 |
| A | PHE277 |
| A | PHE338 |
| A | LYS339 |
| A | HOH678 |
| A | HOH761 |
| A | HOH805 |
| site_id | AC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 468 |
| Chain | Residue |
| A | GLN390 |
| A | ARG393 |
| C | TYR96 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PG4 C 467 |
| Chain | Residue |
| C | PHE265 |
| C | LYS267 |
| C | PHE272 |
| C | GLY273 |
| C | PHE277 |
| C | HOH477 |
| C | HOH1147 |
| site_id | AC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 C 468 |
| Chain | Residue |
| C | MET358 |
| C | ASP359 |
| C | GLN390 |
| C | ARG393 |
| E | TYR96 |
| site_id | AC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO C 469 |
| Chain | Residue |
| C | HIS201 |
| C | HOH790 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PG4 D 467 |
| Chain | Residue |
| D | PHE265 |
| D | LYS267 |
| D | GLY273 |
| D | PHE277 |
| D | PHE338 |
| D | HOH1163 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE EDO D 468 |
| Chain | Residue |
| B | TYR96 |
| D | MET358 |
| D | GLN390 |
| D | HOH806 |
| D | HOH991 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 470 |
| Chain | Residue |
| D | PHE162 |
| D | ASP171 |
| D | ASP176 |
| D | ARG177 |
| site_id | AC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO D 471 |
| Chain | Residue |
| D | TYR96 |
| F | MET358 |
| F | GLN390 |
| F | ARG393 |
| site_id | BC1 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO E 468 |
| Chain | Residue |
| A | TYR96 |
| E | GLN390 |
| site_id | BC2 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE EDO B 467 |
| Chain | Residue |
| B | HOH721 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 468 |
| Chain | Residue |
| B | GLU29 |
| B | ARG31 |
| B | LYS67 |
| B | HOH538 |
| site_id | BC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 469 |
| Chain | Residue |
| B | ASP171 |
| B | ASP176 |
| site_id | BC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PG4 F 467 |
| Chain | Residue |
| F | LEU163 |
| F | GLU165 |
| F | PHE272 |
| F | GLY273 |
| F | PHE277 |
| F | PHE338 |
| F | LYS339 |
| F | ARG442 |
| F | HOH491 |
| F | HOH654 |
| F | HOH717 |
| F | HOH1093 |
| site_id | BC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO F 468 |
| Chain | Residue |
| F | GLY13 |
| F | TYR14 |
| F | ARG346 |
| site_id | BC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO F 469 |
| Chain | Residue |
| F | ARG41 |
| F | PRO51 |
| F | ILE52 |
| site_id | BC8 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO F 470 |
| Chain | Residue |
| F | HIS201 |
| F | HOH863 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 12 |
| Details | ACT_SITE: Proton donor/acceptor => ECO:0000269|PubMed:22123821 |
| Chain | Residue | Details |
| A | GLU161 | |
| E | LYS220 | |
| F | GLU161 | |
| F | LYS220 | |
| A | LYS220 | |
| B | GLU161 | |
| B | LYS220 | |
| C | GLU161 | |
| C | LYS220 | |
| D | GLU161 | |
| D | LYS220 | |
| E | GLU161 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 6 |
| Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:21502315, ECO:0000269|PubMed:21984906, ECO:0000269|PubMed:22123821 |
| Chain | Residue | Details |
| A | CYS276 | |
| B | CYS276 | |
| C | CYS276 | |
| D | CYS276 | |
| E | CYS276 | |
| F | CYS276 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 30 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21502315, ECO:0000269|PubMed:21595445, ECO:0000269|PubMed:21984906, ECO:0007744|PDB:2Q3E, ECO:0007744|PDB:2QG4, ECO:0007744|PDB:3PRJ, ECO:0007744|PDB:3PTZ, ECO:0007744|PDB:3TDK |
| Chain | Residue | Details |
| A | GLY11 | |
| B | CYS276 | |
| C | GLY11 | |
| C | ASP36 | |
| C | ARG41 | |
| C | VAL89 | |
| C | CYS276 | |
| D | GLY11 | |
| D | ASP36 | |
| D | ARG41 | |
| D | VAL89 | |
| A | ASP36 | |
| D | CYS276 | |
| E | GLY11 | |
| E | ASP36 | |
| E | ARG41 | |
| E | VAL89 | |
| E | CYS276 | |
| F | GLY11 | |
| F | ASP36 | |
| F | ARG41 | |
| F | VAL89 | |
| A | ARG41 | |
| F | CYS276 | |
| A | VAL89 | |
| A | CYS276 | |
| B | GLY11 | |
| B | ASP36 | |
| B | ARG41 | |
| B | VAL89 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21502315, ECO:0000269|PubMed:21595445 |
| Chain | Residue | Details |
| A | SER130 | |
| B | SER130 | |
| C | SER130 | |
| D | SER130 | |
| E | SER130 | |
| F | SER130 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:23106432, ECO:0000305|PubMed:21502315, ECO:0000305|PubMed:21595445, ECO:0007744|PDB:2QG4, ECO:0007744|PDB:3PRJ, ECO:0007744|PDB:3PTZ, ECO:0007744|PDB:4EDF |
| Chain | Residue | Details |
| A | GLU161 | |
| C | LYS220 | |
| C | LYS267 | |
| C | PHE338 | |
| D | GLU161 | |
| D | LYS220 | |
| D | LYS267 | |
| D | PHE338 | |
| E | GLU161 | |
| E | LYS220 | |
| E | LYS267 | |
| A | LYS220 | |
| E | PHE338 | |
| F | GLU161 | |
| F | LYS220 | |
| F | LYS267 | |
| F | PHE338 | |
| A | LYS267 | |
| A | PHE338 | |
| B | GLU161 | |
| B | LYS220 | |
| B | LYS267 | |
| B | PHE338 | |
| C | GLU161 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21502315, ECO:0007744|PDB:2Q3E, ECO:0007744|PDB:2QG4 |
| Chain | Residue | Details |
| A | GLU165 | |
| B | GLU165 | |
| C | GLU165 | |
| D | GLU165 | |
| E | GLU165 | |
| F | GLU165 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:23106432, ECO:0000269|PubMed:27966912, ECO:0000305|PubMed:21502315, ECO:0000305|PubMed:21595445, ECO:0007744|PDB:2QG4, ECO:0007744|PDB:3PRJ, ECO:0007744|PDB:3PTZ, ECO:0007744|PDB:4EDF, ECO:0007744|PDB:5TJH |
| Chain | Residue | Details |
| A | ARG260 | |
| B | ARG260 | |
| C | ARG260 | |
| D | ARG260 | |
| E | ARG260 | |
| F | ARG260 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:21502315, ECO:0000269|PubMed:21595445, ECO:0000269|PubMed:21984906, ECO:0000269|PubMed:22123821, ECO:0007744|PDB:2Q3E, ECO:0007744|PDB:2QG4, ECO:0007744|PDB:3PRJ, ECO:0007744|PDB:3PTZ, ECO:0007744|PDB:3TDK |
| Chain | Residue | Details |
| A | ARG346 | |
| B | ARG346 | |
| C | ARG346 | |
| D | ARG346 | |
| E | ARG346 | |
| F | ARG346 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:22123821, ECO:0000269|PubMed:23106432, ECO:0000305|PubMed:21502315, ECO:0000305|PubMed:21595445, ECO:0007744|PDB:2QG4, ECO:0007744|PDB:3KHU, ECO:0007744|PDB:3PRJ, ECO:0007744|PDB:3PTZ, ECO:0007744|PDB:4EDF |
| Chain | Residue | Details |
| A | ARG442 | |
| B | ARG442 | |
| C | ARG442 | |
| D | ARG442 | |
| E | ARG442 | |
| F | ARG442 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 6 |
| Details | MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861 |
| Chain | Residue | Details |
| A | LYS107 | |
| B | LYS107 | |
| C | LYS107 | |
| D | LYS107 | |
| E | LYS107 | |
| F | LYS107 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 6 |
| Details | Annotated By Reference To The Literature 1dli |
| Chain | Residue | Details |
| A | ASP280 | |
| A | ASN224 | |
| A | CYS276 | |
| A | LYS220 | |
| A | SER130 | |
| A | GLU165 |
| site_id | CSA2 |
| Number of Residues | 6 |
| Details | Annotated By Reference To The Literature 1dli |
| Chain | Residue | Details |
| B | ASP280 | |
| B | ASN224 | |
| B | CYS276 | |
| B | LYS220 | |
| B | SER130 | |
| B | GLU165 |
| site_id | CSA3 |
| Number of Residues | 6 |
| Details | Annotated By Reference To The Literature 1dli |
| Chain | Residue | Details |
| C | ASP280 | |
| C | ASN224 | |
| C | CYS276 | |
| C | LYS220 | |
| C | SER130 | |
| C | GLU165 |
| site_id | CSA4 |
| Number of Residues | 6 |
| Details | Annotated By Reference To The Literature 1dli |
| Chain | Residue | Details |
| D | ASP280 | |
| D | ASN224 | |
| D | CYS276 | |
| D | LYS220 | |
| D | SER130 | |
| D | GLU165 |
| site_id | CSA5 |
| Number of Residues | 6 |
| Details | Annotated By Reference To The Literature 1dli |
| Chain | Residue | Details |
| E | ASP280 | |
| E | ASN224 | |
| E | CYS276 | |
| E | LYS220 | |
| E | SER130 | |
| E | GLU165 |
| site_id | CSA6 |
| Number of Residues | 6 |
| Details | Annotated By Reference To The Literature 1dli |
| Chain | Residue | Details |
| F | ASP280 | |
| F | ASN224 | |
| F | CYS276 | |
| F | LYS220 | |
| F | SER130 | |
| F | GLU165 |
