3UNC
Crystal Structure of Bovine Milk Xanthine Dehydrogenase to 1.65A Resolution
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0002197 | cellular_component | xanthine dehydrogenase complex |
| A | 0004854 | molecular_function | xanthine dehydrogenase activity |
| A | 0004855 | molecular_function | xanthine oxidase activity |
| A | 0005506 | molecular_function | iron ion binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005615 | cellular_component | extracellular space |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005777 | cellular_component | peroxisome |
| A | 0009115 | biological_process | xanthine catabolic process |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0030151 | molecular_function | molybdenum ion binding |
| A | 0042803 | molecular_function | protein homodimerization activity |
| A | 0043546 | molecular_function | molybdopterin cofactor binding |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| A | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
| A | 0071949 | molecular_function | FAD binding |
| B | 0002197 | cellular_component | xanthine dehydrogenase complex |
| B | 0004854 | molecular_function | xanthine dehydrogenase activity |
| B | 0004855 | molecular_function | xanthine oxidase activity |
| B | 0005506 | molecular_function | iron ion binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005615 | cellular_component | extracellular space |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005777 | cellular_component | peroxisome |
| B | 0009115 | biological_process | xanthine catabolic process |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0030151 | molecular_function | molybdenum ion binding |
| B | 0042803 | molecular_function | protein homodimerization activity |
| B | 0043546 | molecular_function | molybdopterin cofactor binding |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050660 | molecular_function | flavin adenine dinucleotide binding |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0051537 | molecular_function | 2 iron, 2 sulfur cluster binding |
| B | 0071949 | molecular_function | FAD binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE FES A 1333 |
| Chain | Residue |
| A | GLN112 |
| A | CYS113 |
| A | GLY114 |
| A | CYS116 |
| A | CYS148 |
| A | ARG149 |
| A | CYS150 |
| site_id | AC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FES A 1334 |
| Chain | Residue |
| A | GLY44 |
| A | GLY46 |
| A | GLY47 |
| A | CYS48 |
| A | GLY49 |
| A | CYS51 |
| A | ASN71 |
| A | CYS73 |
| A | GLY42 |
| A | CYS43 |
| site_id | AC3 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE MTE A 1335 |
| Chain | Residue |
| A | GLN112 |
| A | CYS150 |
| A | GLY796 |
| A | GLY797 |
| A | PHE798 |
| A | GLY799 |
| A | ARG912 |
| A | MET1038 |
| A | GLY1039 |
| A | GLN1040 |
| A | ALA1078 |
| A | ALA1079 |
| A | SER1080 |
| A | VAL1081 |
| A | SER1082 |
| A | GLN1194 |
| A | MOS1336 |
| A | HOH2096 |
| A | HOH2097 |
| A | HOH2102 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE MOS A 1336 |
| Chain | Residue |
| A | GLN767 |
| A | GLY799 |
| A | GLU802 |
| A | PHE911 |
| A | ARG912 |
| A | ALA1078 |
| A | ALA1079 |
| A | GLU1261 |
| A | MTE1335 |
| A | HOH1856 |
| site_id | AC5 |
| Number of Residues | 36 |
| Details | BINDING SITE FOR RESIDUE FAD A 1337 |
| Chain | Residue |
| A | GLU45 |
| A | GLY46 |
| A | LYS256 |
| A | LEU257 |
| A | VAL258 |
| A | VAL259 |
| A | GLY260 |
| A | ASN261 |
| A | THR262 |
| A | GLU263 |
| A | ILE264 |
| A | ALA301 |
| A | PHE337 |
| A | ALA338 |
| A | VAL342 |
| A | ALA346 |
| A | SER347 |
| A | GLY350 |
| A | ASN351 |
| A | ILE353 |
| A | THR354 |
| A | SER359 |
| A | ASP360 |
| A | ILE403 |
| A | LEU404 |
| A | LYS422 |
| A | ASP429 |
| A | ASP430 |
| A | GOL1344 |
| A | HOH2032 |
| A | HOH2033 |
| A | HOH2034 |
| A | HOH2035 |
| A | HOH2041 |
| A | HOH2046 |
| A | HOH2083 |
| site_id | AC6 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SAL A 1338 |
| Chain | Residue |
| A | GLU802 |
| A | ARG880 |
| A | PHE914 |
| A | PHE1009 |
| A | THR1010 |
| A | VAL1011 |
| A | LEU1014 |
| A | HOH1856 |
| site_id | AC7 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 1339 |
| Chain | Residue |
| A | HOH2275 |
| A | HOH2277 |
| A | GLY664 |
| A | HIS665 |
| A | ILE666 |
| A | ARG804 |
| A | ILE835 |
| A | ASN869 |
| A | SER906 |
| A | SER907 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL A 1340 |
| Chain | Residue |
| A | GLN1088 |
| A | TYR1091 |
| A | TYR1254 |
| A | HOH1796 |
| site_id | AC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 1341 |
| Chain | Residue |
| A | ASP594 |
| A | PHE604 |
| A | PRO675 |
| A | CYS825 |
| A | MET826 |
| A | HOH1354 |
| A | HOH2342 |
| site_id | BC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1342 |
| Chain | Residue |
| A | LEU648 |
| A | PHE1013 |
| A | HOH1813 |
| A | HOH1814 |
| A | HOH2191 |
| site_id | BC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 1343 |
| Chain | Residue |
| A | LEU580 |
| A | ALA581 |
| A | MET584 |
| A | ARG793 |
| A | TYR1062 |
| A | ILE1063 |
| A | GOL1349 |
| A | HOH1500 |
| A | HOH1501 |
| A | HOH1506 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 1344 |
| Chain | Residue |
| A | GLU45 |
| A | SER1225 |
| A | FAD1337 |
| A | HOH2044 |
| A | HOH2084 |
| A | HOH2086 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1345 |
| Chain | Residue |
| A | GLU45 |
| A | LYS271 |
| A | SER1225 |
| A | HOH1720 |
| A | HOH1723 |
| site_id | BC5 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL A 1346 |
| Chain | Residue |
| A | GLU759 |
| A | MET760 |
| A | ASN785 |
| A | ARG786 |
| A | LEU788 |
| A | HOH1480 |
| A | HOH1483 |
| A | HOH1940 |
| B | LEU1030 |
| B | TYR1062 |
| B | SER1064 |
| site_id | BC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1347 |
| Chain | Residue |
| A | ASP141 |
| A | GLU309 |
| A | LEU313 |
| A | LYS340 |
| A | LYS343 |
| site_id | BC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 1348 |
| Chain | Residue |
| A | GLN561 |
| A | GLY574 |
| A | SER1184 |
| A | SER1185 |
| A | HOH1411 |
| A | HOH1419 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL A 1349 |
| Chain | Residue |
| A | ILE1058 |
| A | ILE1061 |
| A | GOL1343 |
| A | HOH1636 |
| site_id | BC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE CO3 A 1350 |
| Chain | Residue |
| A | ARG839 |
| A | HIS840 |
| A | ILE877 |
| A | THR909 |
| A | ALA910 |
| A | PHE911 |
| A | PHE914 |
| A | GLY915 |
| A | GLN918 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 1351 |
| Chain | Residue |
| A | ALA867 |
| A | SER870 |
| A | ARG871 |
| A | SER874 |
| A | SER907 |
| A | ASN908 |
| site_id | CC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE FES B 1333 |
| Chain | Residue |
| B | GLN112 |
| B | CYS113 |
| B | GLY114 |
| B | CYS116 |
| B | CYS148 |
| B | ARG149 |
| B | CYS150 |
| site_id | CC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FES B 1334 |
| Chain | Residue |
| B | GLY42 |
| B | CYS43 |
| B | GLY44 |
| B | GLY46 |
| B | GLY47 |
| B | CYS48 |
| B | GLY49 |
| B | CYS51 |
| B | ASN71 |
| B | CYS73 |
| site_id | CC4 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE MTE B 1335 |
| Chain | Residue |
| B | GLN112 |
| B | CYS150 |
| B | GLY796 |
| B | GLY797 |
| B | PHE798 |
| B | GLY799 |
| B | ARG912 |
| B | MET1038 |
| B | GLY1039 |
| B | GLN1040 |
| B | ALA1078 |
| B | ALA1079 |
| B | SER1080 |
| B | VAL1081 |
| B | SER1082 |
| B | GLN1194 |
| B | MOS1336 |
| B | HOH1602 |
| B | HOH1603 |
| B | HOH1605 |
| site_id | CC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE MOS B 1336 |
| Chain | Residue |
| B | GLN767 |
| B | GLY799 |
| B | GLU802 |
| B | PHE911 |
| B | ARG912 |
| B | ALA1078 |
| B | ALA1079 |
| B | GLU1261 |
| B | MTE1335 |
| B | HOH1963 |
| site_id | CC6 |
| Number of Residues | 35 |
| Details | BINDING SITE FOR RESIDUE FAD B 1337 |
| Chain | Residue |
| B | GLU45 |
| B | GLY46 |
| B | LEU257 |
| B | VAL258 |
| B | VAL259 |
| B | GLY260 |
| B | ASN261 |
| B | THR262 |
| B | GLU263 |
| B | ILE264 |
| B | ALA301 |
| B | PHE337 |
| B | ALA338 |
| B | VAL342 |
| B | ALA346 |
| B | SER347 |
| B | GLY350 |
| B | ASN351 |
| B | ILE353 |
| B | THR354 |
| B | SER359 |
| B | ASP360 |
| B | ILE403 |
| B | LEU404 |
| B | LYS422 |
| B | ASP429 |
| B | ASP430 |
| B | GOL1344 |
| B | HOH1777 |
| B | HOH1836 |
| B | HOH1838 |
| B | HOH1839 |
| B | HOH1840 |
| B | HOH1861 |
| B | HOH2296 |
| site_id | CC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SAL B 1338 |
| Chain | Residue |
| B | GLU802 |
| B | ARG880 |
| B | PHE914 |
| B | PHE1009 |
| B | THR1010 |
| B | LEU1014 |
| B | HOH1449 |
| B | HOH1963 |
| site_id | CC8 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL B 1339 |
| Chain | Residue |
| B | CYS662 |
| B | GLY664 |
| B | HIS665 |
| B | ILE666 |
| B | ARG804 |
| B | ILE835 |
| B | ASN869 |
| B | SER906 |
| B | SER907 |
| B | HOH1697 |
| B | HOH1699 |
| site_id | CC9 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 1340 |
| Chain | Residue |
| B | GLN1088 |
| B | TYR1091 |
| B | ILE1253 |
| B | TYR1254 |
| site_id | DC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 1341 |
| Chain | Residue |
| B | ASP594 |
| B | PHE604 |
| B | PRO675 |
| B | CYS825 |
| B | MET826 |
| B | HOH2075 |
| B | HOH2165 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 1342 |
| Chain | Residue |
| B | PHE1013 |
| B | HOH1513 |
| B | HOH1516 |
| B | HOH1517 |
| site_id | DC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL B 1343 |
| Chain | Residue |
| B | LEU580 |
| B | ALA581 |
| B | MET584 |
| B | ARG793 |
| B | TYR1062 |
| B | ILE1063 |
| B | HOH1622 |
| B | HOH2254 |
| B | HOH2257 |
| B | HOH2258 |
| site_id | DC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 1344 |
| Chain | Residue |
| B | GLU45 |
| B | SER1225 |
| B | FAD1337 |
| B | HOH1400 |
| B | HOH1403 |
| B | HOH1778 |
| site_id | DC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 1345 |
| Chain | Residue |
| B | GLU45 |
| B | PHE270 |
| B | LYS271 |
| B | SER1225 |
| B | HOH1402 |
| B | HOH2141 |
| site_id | DC6 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL B 1346 |
| Chain | Residue |
| A | LEU1030 |
| A | TYR1062 |
| A | SER1064 |
| B | GLU759 |
| B | MET760 |
| B | ASN785 |
| B | ARG786 |
| B | LEU788 |
| B | HOH1487 |
| B | HOH1509 |
| B | HOH1634 |
| site_id | DC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 1347 |
| Chain | Residue |
| B | GLN561 |
| B | GLY574 |
| B | SER1184 |
| B | SER1185 |
| B | PRO1188 |
| B | HOH2223 |
| B | HOH2229 |
| site_id | DC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 1348 |
| Chain | Residue |
| B | ASP141 |
| B | GLN144 |
| B | GLU309 |
| B | LEU313 |
| B | LYS340 |
| B | LYS343 |
| B | HOH1876 |
| site_id | DC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 1349 |
| Chain | Residue |
| B | PHE549 |
| B | LYS994 |
| B | GLU1163 |
| B | ASP1170 |
| B | HIS1171 |
| B | LYS1172 |
| site_id | EC1 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 1350 |
| Chain | Residue |
| A | LEU788 |
| A | ARG790 |
| A | GLU1065 |
| A | SER1067 |
| A | ASN1069 |
| B | ARG790 |
| B | GLU1065 |
| B | SER1067 |
| B | ASN1069 |
| site_id | EC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 1351 |
| Chain | Residue |
| B | PRO937 |
| B | ALA938 |
| B | LEU998 |
| B | ASP1276 |
| B | HOH1749 |
| B | HOH1754 |
| site_id | EC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE CO3 B 1352 |
| Chain | Residue |
| B | ARG839 |
| B | HIS840 |
| B | ILE877 |
| B | THR909 |
| B | ALA910 |
| B | PHE911 |
| B | PHE914 |
| B | GLY915 |
| B | GLN918 |
| site_id | EC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 1353 |
| Chain | Residue |
| B | ALA867 |
| B | SER870 |
| B | ARG871 |
| B | SER874 |
| B | SER907 |
| B | ASN908 |
Functional Information from PROSITE/UniProt
| site_id | PS00197 |
| Number of Residues | 9 |
| Details | 2FE2S_FER_1 2Fe-2S ferredoxin-type iron-sulfur binding region signature. CGEGGCGAC |
| Chain | Residue | Details |
| A | CYS43-CYS51 |
| site_id | PS00559 |
| Number of Residues | 36 |
| Details | MOLYBDOPTERIN_EUK Eukaryotic molybdopterin oxidoreductases signature. GFggKetrstlvsvava..LaayKTghpVrCmlDRneD |
| Chain | Residue | Details |
| A | GLY797-ASP832 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 174 |
| Details | Domain: {"description":"2Fe-2S ferredoxin-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00465","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 370 |
| Details | Domain: {"description":"FAD-binding PCMH-type","evidences":[{"source":"PROSITE-ProRule","id":"PRU00718","evidenceCode":"ECO:0000255"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Active site: {"description":"Proton acceptor","evidences":[{"source":"PubMed","id":"15148401","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 24 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"12421831","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15148401","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19109252","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 30 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"12421831","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15148401","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | Binding site: {} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 3 |
| Details | M-CSA 139 |
| Chain | Residue | Details |
| A | GLU802 | electrostatic stabiliser, hydrogen bond acceptor |
| A | ARG880 | electrostatic stabiliser, hydrogen bond donor |
| A | GLU1261 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
| site_id | MCSA2 |
| Number of Residues | 3 |
| Details | M-CSA 139 |
| Chain | Residue | Details |
| B | GLU802 | electrostatic stabiliser, hydrogen bond acceptor |
| B | ARG880 | electrostatic stabiliser, hydrogen bond donor |
| B | GLU1261 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
