3BDJ
Crystal Structure of Bovine Milk Xanthine Dehydrogenase with a Covalently Bound Oxipurinol Inhibitor
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 | 6 |
| Details | BINDING SITE FOR RESIDUE CA A5301 |
| Chain | Residue |
| A | ALA867 |
| A | SER870 |
| A | ARG871 |
| A | SER874 |
| A | SER907 |
| A | ASN908 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE FES A3001 |
| Chain | Residue |
| A | CYS116 |
| A | CYS148 |
| A | ARG149 |
| A | CYS150 |
| A | GLN112 |
| A | CYS113 |
| A | GLY114 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FES A3002 |
| Chain | Residue |
| A | GLY42 |
| A | CYS43 |
| A | GLY44 |
| A | GLY46 |
| A | GLY47 |
| A | CYS48 |
| A | GLY49 |
| A | CYS51 |
| A | ASN71 |
| A | CYS73 |
| site_id | AC4 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE MTE A3003 |
| 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 | GLU1261 |
| A | MOW3004 |
| A | 1415101 |
| A | HOH5631 |
| A | HOH5633 |
| A | HOH5638 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MOW A3004 |
| Chain | Residue |
| A | GLN767 |
| A | GLY799 |
| A | PHE911 |
| A | ARG912 |
| A | ALA1078 |
| A | GLU1261 |
| A | MTE3003 |
| A | 1415101 |
| site_id | AC6 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE FAD A3005 |
| Chain | Residue |
| A | GLU45 |
| A | GLY46 |
| A | LEU74 |
| 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 | HOH5618 |
| A | HOH5980 |
| A | HOH5982 |
| A | HOH6000 |
| site_id | AC7 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE 141 A5101 |
| Chain | Residue |
| A | GLU802 |
| A | ARG880 |
| A | PHE914 |
| A | PHE1009 |
| A | THR1010 |
| A | ALA1078 |
| A | ALA1079 |
| A | GLU1261 |
| A | MTE3003 |
| A | MOW3004 |
| A | HOH5479 |
| A | HOH5480 |
| A | HOH5887 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A5005 |
| Chain | Residue |
| A | CYS662 |
| A | HIS665 |
| A | ILE666 |
| A | ARG804 |
| A | ASN869 |
| A | SER906 |
| A | SER907 |
| A | HOH5402 |
| site_id | AC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A5006 |
| Chain | Residue |
| A | ASP594 |
| A | PHE604 |
| A | CYS825 |
| A | MET826 |
| A | HOH5719 |
| site_id | BC1 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE GOL A5007 |
| Chain | Residue |
| A | GLU759 |
| A | MET760 |
| A | ASN785 |
| A | ARG786 |
| A | LEU788 |
| A | HOH5756 |
| A | HOH5757 |
| A | HOH5927 |
| B | LEU1030 |
| B | TYR1062 |
| B | SER1064 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE CO3 A5201 |
| Chain | Residue |
| A | ARG839 |
| A | HIS840 |
| A | ILE877 |
| A | THR909 |
| A | ALA910 |
| A | PHE911 |
| A | PHE914 |
| A | GLY915 |
| A | GLN918 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B5302 |
| Chain | Residue |
| B | ALA867 |
| B | SER870 |
| B | ARG871 |
| B | SER874 |
| B | SER907 |
| B | ASN908 |
| site_id | BC4 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE FES B4001 |
| Chain | Residue |
| B | GLN112 |
| B | CYS113 |
| B | GLY114 |
| B | CYS116 |
| B | CYS148 |
| B | ARG149 |
| B | CYS150 |
| B | LEU744 |
| site_id | BC5 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FES B4002 |
| Chain | Residue |
| B | GLY42 |
| B | CYS43 |
| B | GLY44 |
| B | GLY46 |
| B | GLY47 |
| B | CYS48 |
| B | GLY49 |
| B | CYS51 |
| B | ASN71 |
| B | CYS73 |
| site_id | BC6 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE MTE B4003 |
| 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 | GLU1261 |
| B | MOW4004 |
| B | 1415102 |
| B | HOH5485 |
| B | HOH5490 |
| B | HOH5492 |
| site_id | BC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE MOW B4004 |
| Chain | Residue |
| B | GLN767 |
| B | GLY799 |
| B | PHE911 |
| B | ARG912 |
| B | ALA1078 |
| B | GLU1261 |
| B | MTE4003 |
| B | 1415102 |
| site_id | BC8 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE FAD B4005 |
| Chain | Residue |
| B | GLU45 |
| B | GLY46 |
| B | LEU74 |
| B | LYS256 |
| 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 | HOH5751 |
| B | HOH5755 |
| B | HOH5759 |
| B | HOH5974 |
| site_id | BC9 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE 141 B5102 |
| Chain | Residue |
| B | GLU802 |
| B | ARG880 |
| B | PHE914 |
| B | PHE1009 |
| B | THR1010 |
| B | ALA1078 |
| B | ALA1079 |
| B | GLU1261 |
| B | MTE4003 |
| B | MOW4004 |
| B | HOH5340 |
| B | HOH5341 |
| B | HOH5342 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B5001 |
| Chain | Residue |
| B | ASP594 |
| B | PHE604 |
| B | PRO675 |
| B | CYS825 |
| B | MET826 |
| B | HOH5635 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B5002 |
| Chain | Residue |
| B | CYS662 |
| B | HIS665 |
| B | ILE666 |
| B | ARG804 |
| B | ILE835 |
| B | ASN869 |
| B | SER906 |
| B | SER907 |
| site_id | CC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B5003 |
| Chain | Residue |
| B | GLN561 |
| B | GLY574 |
| B | SER1184 |
| B | SER1185 |
| B | HOH5375 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B5004 |
| Chain | Residue |
| B | LEU580 |
| B | TYR1062 |
| B | ILE1063 |
| B | HOH5507 |
| B | HOH5521 |
| site_id | CC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE CO3 B5202 |
| Chain | Residue |
| B | ARG839 |
| B | HIS840 |
| B | ILE877 |
| B | THR909 |
| B | ALA910 |
| B | PHE911 |
| B | PHE914 |
| B | GLY915 |
| B | GLN918 |
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 | 2 |
| Details | ACT_SITE: Proton acceptor => ECO:0000269|PubMed:15148401 |
| Chain | Residue | Details |
| A | GLU1261 | |
| B | GLU1261 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 24 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401, ECO:0000269|PubMed:19109252 |
| Chain | Residue | Details |
| A | CYS43 | |
| A | PHE798 | |
| A | ARG912 | |
| A | ALA1079 | |
| B | CYS43 | |
| B | CYS48 | |
| B | CYS51 | |
| B | CYS73 | |
| B | CYS113 | |
| B | CYS116 | |
| B | CYS148 | |
| A | CYS48 | |
| B | CYS150 | |
| B | GLN767 | |
| B | PHE798 | |
| B | ARG912 | |
| B | ALA1079 | |
| A | CYS51 | |
| A | CYS73 | |
| A | CYS113 | |
| A | CYS116 | |
| A | CYS148 | |
| A | CYS150 | |
| A | GLN767 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:12421831, ECO:0000269|PubMed:15148401 |
| Chain | Residue | Details |
| A | LEU257 | |
| B | ASP360 | |
| B | LEU404 | |
| B | LYS422 | |
| A | PHE337 | |
| A | SER347 | |
| A | ASP360 | |
| A | LEU404 | |
| A | LYS422 | |
| B | LEU257 | |
| B | PHE337 | |
| B | SER347 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | BINDING: |
| Chain | Residue | Details |
| A | GLU802 | |
| A | ARG880 | |
| A | PHE914 | |
| A | THR1010 | |
| B | GLU802 | |
| B | ARG880 | |
| B | PHE914 | |
| B | THR1010 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1fiq |
| Chain | Residue | Details |
| A | GLU1261 |
| site_id | CSA2 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 1fiq |
| Chain | Residue | Details |
| B | GLU1261 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1fiq |
| Chain | Residue | Details |
| A | ARG912 | |
| A | GLN767 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 1fiq |
| Chain | Residue | Details |
| B | ARG912 | |
| B | GLN767 |
| 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 |
