5FV9
Crystal structure of GalNAc-T2 in complex with compound 16d
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000139 | cellular_component | Golgi membrane |
| A | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005789 | cellular_component | endoplasmic reticulum membrane |
| A | 0005794 | cellular_component | Golgi apparatus |
| A | 0005795 | cellular_component | Golgi stack |
| A | 0006486 | biological_process | protein glycosylation |
| A | 0006493 | biological_process | protein O-linked glycosylation |
| A | 0016020 | cellular_component | membrane |
| A | 0016266 | biological_process | O-glycan processing |
| A | 0016757 | molecular_function | glycosyltransferase activity |
| A | 0018242 | biological_process | protein O-linked glycosylation via serine |
| A | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| A | 0030145 | molecular_function | manganese ion binding |
| A | 0030246 | molecular_function | carbohydrate binding |
| A | 0032580 | cellular_component | Golgi cisterna membrane |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0048471 | cellular_component | perinuclear region of cytoplasm |
| A | 0051604 | biological_process | protein maturation |
| B | 0000139 | cellular_component | Golgi membrane |
| B | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005789 | cellular_component | endoplasmic reticulum membrane |
| B | 0005794 | cellular_component | Golgi apparatus |
| B | 0005795 | cellular_component | Golgi stack |
| B | 0006486 | biological_process | protein glycosylation |
| B | 0006493 | biological_process | protein O-linked glycosylation |
| B | 0016020 | cellular_component | membrane |
| B | 0016266 | biological_process | O-glycan processing |
| B | 0016757 | molecular_function | glycosyltransferase activity |
| B | 0018242 | biological_process | protein O-linked glycosylation via serine |
| B | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| B | 0030145 | molecular_function | manganese ion binding |
| B | 0030246 | molecular_function | carbohydrate binding |
| B | 0032580 | cellular_component | Golgi cisterna membrane |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0048471 | cellular_component | perinuclear region of cytoplasm |
| B | 0051604 | biological_process | protein maturation |
| C | 0000139 | cellular_component | Golgi membrane |
| C | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| C | 0005515 | molecular_function | protein binding |
| C | 0005576 | cellular_component | extracellular region |
| C | 0005789 | cellular_component | endoplasmic reticulum membrane |
| C | 0005794 | cellular_component | Golgi apparatus |
| C | 0005795 | cellular_component | Golgi stack |
| C | 0006486 | biological_process | protein glycosylation |
| C | 0006493 | biological_process | protein O-linked glycosylation |
| C | 0016020 | cellular_component | membrane |
| C | 0016266 | biological_process | O-glycan processing |
| C | 0016757 | molecular_function | glycosyltransferase activity |
| C | 0018242 | biological_process | protein O-linked glycosylation via serine |
| C | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| C | 0030145 | molecular_function | manganese ion binding |
| C | 0030246 | molecular_function | carbohydrate binding |
| C | 0032580 | cellular_component | Golgi cisterna membrane |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0048471 | cellular_component | perinuclear region of cytoplasm |
| C | 0051604 | biological_process | protein maturation |
| D | 0000139 | cellular_component | Golgi membrane |
| D | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| D | 0005515 | molecular_function | protein binding |
| D | 0005576 | cellular_component | extracellular region |
| D | 0005789 | cellular_component | endoplasmic reticulum membrane |
| D | 0005794 | cellular_component | Golgi apparatus |
| D | 0005795 | cellular_component | Golgi stack |
| D | 0006486 | biological_process | protein glycosylation |
| D | 0006493 | biological_process | protein O-linked glycosylation |
| D | 0016020 | cellular_component | membrane |
| D | 0016266 | biological_process | O-glycan processing |
| D | 0016757 | molecular_function | glycosyltransferase activity |
| D | 0018242 | biological_process | protein O-linked glycosylation via serine |
| D | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| D | 0030145 | molecular_function | manganese ion binding |
| D | 0030246 | molecular_function | carbohydrate binding |
| D | 0032580 | cellular_component | Golgi cisterna membrane |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0048471 | cellular_component | perinuclear region of cytoplasm |
| D | 0051604 | biological_process | protein maturation |
| E | 0000139 | cellular_component | Golgi membrane |
| E | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| E | 0005515 | molecular_function | protein binding |
| E | 0005576 | cellular_component | extracellular region |
| E | 0005789 | cellular_component | endoplasmic reticulum membrane |
| E | 0005794 | cellular_component | Golgi apparatus |
| E | 0005795 | cellular_component | Golgi stack |
| E | 0006486 | biological_process | protein glycosylation |
| E | 0006493 | biological_process | protein O-linked glycosylation |
| E | 0016020 | cellular_component | membrane |
| E | 0016266 | biological_process | O-glycan processing |
| E | 0016757 | molecular_function | glycosyltransferase activity |
| E | 0018242 | biological_process | protein O-linked glycosylation via serine |
| E | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| E | 0030145 | molecular_function | manganese ion binding |
| E | 0030246 | molecular_function | carbohydrate binding |
| E | 0032580 | cellular_component | Golgi cisterna membrane |
| E | 0046872 | molecular_function | metal ion binding |
| E | 0048471 | cellular_component | perinuclear region of cytoplasm |
| E | 0051604 | biological_process | protein maturation |
| F | 0000139 | cellular_component | Golgi membrane |
| F | 0004653 | molecular_function | polypeptide N-acetylgalactosaminyltransferase activity |
| F | 0005515 | molecular_function | protein binding |
| F | 0005576 | cellular_component | extracellular region |
| F | 0005789 | cellular_component | endoplasmic reticulum membrane |
| F | 0005794 | cellular_component | Golgi apparatus |
| F | 0005795 | cellular_component | Golgi stack |
| F | 0006486 | biological_process | protein glycosylation |
| F | 0006493 | biological_process | protein O-linked glycosylation |
| F | 0016020 | cellular_component | membrane |
| F | 0016266 | biological_process | O-glycan processing |
| F | 0016757 | molecular_function | glycosyltransferase activity |
| F | 0018242 | biological_process | protein O-linked glycosylation via serine |
| F | 0018243 | biological_process | protein O-linked glycosylation via threonine |
| F | 0030145 | molecular_function | manganese ion binding |
| F | 0030246 | molecular_function | carbohydrate binding |
| F | 0032580 | cellular_component | Golgi cisterna membrane |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0048471 | cellular_component | perinuclear region of cytoplasm |
| F | 0051604 | biological_process | protein maturation |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE UDP A 1570 |
| Chain | Residue |
| A | THR143 |
| A | ARG362 |
| A | MN1571 |
| A | HOH2084 |
| A | HOH2164 |
| A | HOH2166 |
| A | HIS145 |
| A | ASP176 |
| A | ARG201 |
| A | LEU204 |
| A | ASP224 |
| A | HIS226 |
| A | VAL330 |
| A | HIS359 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN A 1571 |
| Chain | Residue |
| A | ASP224 |
| A | HIS226 |
| A | HIS359 |
| A | UDP1570 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1572 |
| Chain | Residue |
| A | GLY535 |
| A | SER536 |
| A | ASN537 |
| site_id | AC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO A 1573 |
| Chain | Residue |
| A | TYR177 |
| A | SER178 |
| A | ASN179 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 1575 |
| Chain | Residue |
| A | TYR99 |
| A | LYS103 |
| A | HOH2024 |
| site_id | AC6 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE Y6W B 1570 |
| Chain | Residue |
| B | THR143 |
| B | HIS145 |
| B | ASP176 |
| B | ARG201 |
| B | LEU204 |
| B | SER207 |
| B | ASP224 |
| B | HIS226 |
| B | VAL330 |
| B | GLU334 |
| B | ARG362 |
| B | MN1571 |
| B | UDP1572 |
| B | HOH2168 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN B 1571 |
| Chain | Residue |
| B | ASP224 |
| B | HIS226 |
| B | HIS359 |
| B | Y6W1570 |
| B | UDP1572 |
| site_id | AC8 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE UDP B 1572 |
| Chain | Residue |
| B | THR143 |
| B | PHE144 |
| B | HIS145 |
| B | ASP176 |
| B | ARG201 |
| B | LEU204 |
| B | ASP224 |
| B | HIS226 |
| B | HIS359 |
| B | ARG362 |
| B | Y6W1570 |
| B | MN1571 |
| B | HOH2051 |
| site_id | AC9 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO B 1573 |
| Chain | Residue |
| B | TYR408 |
| B | GLY409 |
| site_id | BC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO B 1574 |
| Chain | Residue |
| B | GLU481 |
| B | ALA483 |
| B | LYS491 |
| B | MET493 |
| site_id | BC2 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE UDP C 1570 |
| Chain | Residue |
| C | THR143 |
| C | HIS145 |
| C | ASP176 |
| C | ARG201 |
| C | LEU204 |
| C | SER207 |
| C | ASP224 |
| C | HIS226 |
| C | VAL330 |
| C | HIS359 |
| C | ARG362 |
| C | MN1571 |
| C | HOH2058 |
| C | HOH2059 |
| C | HOH2132 |
| site_id | BC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN C 1571 |
| Chain | Residue |
| C | ASP224 |
| C | HIS226 |
| C | HIS359 |
| C | UDP1570 |
| site_id | BC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 1572 |
| Chain | Residue |
| C | LYS271 |
| C | LYS302 |
| C | VAL433 |
| site_id | BC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO C 1573 |
| Chain | Residue |
| C | ASP517 |
| C | SER518 |
| C | ARG519 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL C 1574 |
| Chain | Residue |
| C | TYR408 |
| C | GLY409 |
| C | HOH2303 |
| C | HOH2304 |
| F | GLN412 |
| site_id | BC7 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE UDP D 1555 |
| Chain | Residue |
| D | ARG201 |
| D | GLY203 |
| D | LEU204 |
| D | SER207 |
| D | ASP224 |
| D | HIS226 |
| D | VAL330 |
| D | GLU334 |
| D | HIS359 |
| D | ARG362 |
| D | MN1556 |
| D | HOH2055 |
| D | HOH2180 |
| D | THR143 |
| D | PHE144 |
| D | HIS145 |
| D | ASP176 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MN D 1556 |
| Chain | Residue |
| D | ASP224 |
| D | HIS226 |
| D | HIS359 |
| D | UDP1555 |
| site_id | BC9 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE UDP E 1570 |
| Chain | Residue |
| E | THR143 |
| E | HIS145 |
| E | ASP176 |
| E | ARG201 |
| E | LEU204 |
| E | SER207 |
| E | ASP224 |
| E | HIS226 |
| E | VAL330 |
| E | HIS359 |
| E | ARG362 |
| E | MN1571 |
| E | Y6W1572 |
| E | HOH2053 |
| E | HOH2054 |
| E | HOH2121 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN E 1571 |
| Chain | Residue |
| E | ASP224 |
| E | HIS226 |
| E | HIS359 |
| E | UDP1570 |
| E | Y6W1572 |
| site_id | CC2 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE Y6W E 1572 |
| Chain | Residue |
| E | THR143 |
| E | PHE144 |
| E | HIS145 |
| E | ASP176 |
| E | ARG201 |
| E | SER207 |
| E | HIS226 |
| E | VAL330 |
| E | GLU334 |
| E | ARG362 |
| E | UDP1570 |
| E | MN1571 |
| E | HOH2109 |
| E | HOH2181 |
| site_id | CC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE EDO E 1573 |
| Chain | Residue |
| A | HOH2158 |
| E | ASN198 |
| E | ASP199 |
| E | ARG200 |
| E | GLU202 |
| E | ARG210 |
| E | HOH2101 |
| site_id | CC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE EDO E 1574 |
| Chain | Residue |
| E | TRP343 |
| E | ASN432 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE EDO E 1575 |
| Chain | Residue |
| E | TYR177 |
| E | SER178 |
| E | ASN179 |
| site_id | CC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO E 1576 |
| Chain | Residue |
| E | GLU481 |
| E | LYS491 |
| E | HIS492 |
| E | MET493 |
| site_id | CC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE UDP F 1570 |
| Chain | Residue |
| F | THR143 |
| F | PHE144 |
| F | HIS145 |
| F | ASP176 |
| F | ARG201 |
| F | LEU204 |
| F | ASP224 |
| F | HIS226 |
| F | HIS359 |
| F | ARG362 |
| F | MN1571 |
| F | Y6W1572 |
| F | HOH2063 |
| site_id | CC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MN F 1571 |
| Chain | Residue |
| F | ASP224 |
| F | HIS226 |
| F | HIS359 |
| F | UDP1570 |
| F | Y6W1572 |
| site_id | CC9 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE Y6W F 1572 |
| Chain | Residue |
| F | THR143 |
| F | PHE144 |
| F | ASP176 |
| F | ARG201 |
| F | ASP224 |
| F | HIS226 |
| F | VAL330 |
| F | GLU334 |
| F | ARG362 |
| F | UDP1570 |
| F | MN1571 |
| F | HOH2097 |
| site_id | DC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO F 1573 |
| Chain | Residue |
| F | ARG502 |
| F | SER536 |
| F | ASN537 |
| F | HOH2199 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO F 1574 |
| Chain | Residue |
| F | PRO407 |
| F | TYR408 |
| F | GLY409 |
| F | HOH2200 |
| site_id | DC3 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE EDO F 1575 |
| Chain | Residue |
| F | ARG514 |
| F | ASP517 |
| F | SER518 |
| F | ARG519 |
| site_id | DC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL F 1576 |
| Chain | Residue |
| F | ASP199 |
| F | GLU202 |
| F | ARG210 |
| F | HOH2202 |
| site_id | DC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL F 1577 |
| Chain | Residue |
| E | ARG514 |
| E | ASP517 |
| E | ARG519 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 30 |
| Details | TOPO_DOM: Cytoplasmic => ECO:0000255 |
| Chain | Residue | Details |
| A | MET1-ARG6 | |
| B | MET1-ARG6 | |
| C | MET1-ARG6 | |
| D | MET1-ARG6 | |
| E | MET1-ARG6 | |
| F | MET1-ARG6 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 102 |
| Details | TRANSMEM: Helical; Signal-anchor for type II membrane protein => ECO:0000255 |
| Chain | Residue | Details |
| A | MET7-TYR24 | |
| B | MET7-TYR24 | |
| C | MET7-TYR24 | |
| D | MET7-TYR24 | |
| E | MET7-TYR24 | |
| F | MET7-TYR24 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 3276 |
| Details | TOPO_DOM: Lumenal => ECO:0000255 |
| Chain | Residue | Details |
| A | SER25-GLN571 | |
| B | SER25-GLN571 | |
| C | SER25-GLN571 | |
| D | SER25-GLN571 | |
| E | SER25-GLN571 | |
| F | SER25-GLN571 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 42 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:24954443, ECO:0000269|PubMed:25939779, ECO:0007744|PDB:2FFU, ECO:0007744|PDB:2FFV, ECO:0007744|PDB:4D0T, ECO:0007744|PDB:4D11, ECO:0007744|PDB:5AJP, ECO:0007744|PDB:5FV9 |
| Chain | Residue | Details |
| A | THR143 | |
| B | ARG201 | |
| B | SER225 | |
| B | TRP331 | |
| B | ARG362 | |
| B | HIS365 | |
| C | THR143 | |
| C | ASP176 | |
| C | ARG201 | |
| C | SER225 | |
| C | TRP331 | |
| A | ASP176 | |
| C | ARG362 | |
| C | HIS365 | |
| D | THR143 | |
| D | ASP176 | |
| D | ARG201 | |
| D | SER225 | |
| D | TRP331 | |
| D | ARG362 | |
| D | HIS365 | |
| E | THR143 | |
| A | ARG201 | |
| E | ASP176 | |
| E | ARG201 | |
| E | SER225 | |
| E | TRP331 | |
| E | ARG362 | |
| E | HIS365 | |
| F | THR143 | |
| F | ASP176 | |
| F | ARG201 | |
| F | SER225 | |
| A | SER225 | |
| F | TRP331 | |
| F | ARG362 | |
| F | HIS365 | |
| A | TRP331 | |
| A | ARG362 | |
| A | HIS365 | |
| B | THR143 | |
| B | ASP176 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 18 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:24954443, ECO:0000269|PubMed:25939779, ECO:0007744|PDB:2FFU, ECO:0007744|PDB:2FFV, ECO:0007744|PDB:4D0T, ECO:0007744|PDB:4D0Z, ECO:0007744|PDB:4D11, ECO:0007744|PDB:5AJP, ECO:0007744|PDB:5FV9 |
| Chain | Residue | Details |
| A | ASP224 | |
| D | ASP224 | |
| D | HIS226 | |
| D | HIS359 | |
| E | ASP224 | |
| E | HIS226 | |
| E | HIS359 | |
| F | ASP224 | |
| F | HIS226 | |
| F | HIS359 | |
| A | HIS226 | |
| A | HIS359 | |
| B | ASP224 | |
| B | HIS226 | |
| B | HIS359 | |
| C | ASP224 | |
| C | HIS226 | |
| C | HIS359 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 6 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:16434399, ECO:0000269|PubMed:24954443, ECO:0000269|PubMed:25939779, ECO:0007744|PDB:2FFU, ECO:0007744|PDB:2FFV, ECO:0007744|PDB:4D0T, ECO:0007744|PDB:4D0Z, ECO:0007744|PDB:4D11, ECO:0007744|PDB:5AJN, ECO:0007744|PDB:5AJO, ECO:0007744|PDB:5AJP, ECO:0007744|PDB:5FV9, ECO:0007744|PDB:5NDF, ECO:0007744|PDB:6EGS |
| Chain | Residue | Details |
| A | TYR367 | |
| B | TYR367 | |
| C | TYR367 | |
| D | TYR367 | |
| E | TYR367 | |
| F | TYR367 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 6 |
| Details | SITE: Not glycosylated |
| Chain | Residue | Details |
| A | ASP516 | |
| B | ASP516 | |
| C | ASP516 | |
| D | ASP516 | |
| E | ASP516 | |
| F | ASP516 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 6 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| A | SER536 | |
| B | SER536 | |
| C | SER536 | |
| D | SER536 | |
| E | SER536 | |
| F | SER536 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 6 |
| Details | CARBOHYD: O-linked (Xyl...) (chondroitin sulfate) serine => ECO:0000269|PubMed:37453717 |
| Chain | Residue | Details |
| A | SER29 | |
| B | SER29 | |
| C | SER29 | |
| D | SER29 | |
| E | SER29 | |
| F | SER29 |
