1V97
Crystal Structure of Bovine Milk Xanthine Dehydrogenase FYX-051 bound form
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 A 3008 |
| Chain | Residue |
| A | ALA867 |
| A | SER870 |
| A | ARG871 |
| A | SER874 |
| A | SER907 |
| A | ASN908 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 4008 |
| Chain | Residue |
| B | SER874 |
| B | SER907 |
| B | ASN908 |
| B | ALA867 |
| B | SER870 |
| B | ARG871 |
| site_id | AC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE FES A 3001 |
| Chain | Residue |
| A | GLN112 |
| A | CYS113 |
| A | GLY114 |
| A | CYS116 |
| A | CYS148 |
| A | ARG149 |
| A | CYS150 |
| site_id | AC4 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FES A 3002 |
| Chain | Residue |
| A | GLY42 |
| A | CYS43 |
| A | GLY44 |
| A | GLY46 |
| A | GLY47 |
| A | CYS48 |
| A | GLY49 |
| A | CYS51 |
| A | ASN71 |
| A | CYS73 |
| site_id | AC5 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE MTE A 3003 |
| 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 | MOS3004 |
| A | HOH5020 |
| A | HOH5028 |
| A | HOH5052 |
| A | HOH5111 |
| site_id | AC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MOS A 3004 |
| Chain | Residue |
| A | GLN767 |
| A | GLY799 |
| A | PHE911 |
| A | ARG912 |
| A | ALA1078 |
| A | ALA1079 |
| A | GLU1261 |
| A | MTE3003 |
| A | FYX3006 |
| site_id | AC7 |
| Number of Residues | 34 |
| Details | BINDING SITE FOR RESIDUE FAD A 3005 |
| 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 | ALA346 |
| A | SER347 |
| A | GLY350 |
| A | ASN351 |
| A | ILE353 |
| A | THR354 |
| A | SER359 |
| A | ASP360 |
| A | ILE403 |
| A | LEU404 |
| A | LYS422 |
| A | ASP429 |
| A | HOH5200 |
| A | HOH5235 |
| A | HOH5241 |
| A | HOH5364 |
| A | HOH5379 |
| A | HOH5584 |
| A | HOH6010 |
| A | HOH6062 |
| site_id | AC8 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FYX A 3006 |
| Chain | Residue |
| A | PHE914 |
| A | PHE1009 |
| A | LEU1014 |
| A | ALA1079 |
| A | GLU1261 |
| A | MOS3004 |
| A | HOH5593 |
| A | HOH5936 |
| A | ASN768 |
| A | LYS771 |
| A | GLU802 |
| A | LEU873 |
| A | ARG880 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE FES B 4001 |
| Chain | Residue |
| B | GLN112 |
| B | CYS113 |
| B | GLY114 |
| B | CYS116 |
| B | CYS148 |
| B | ARG149 |
| B | CYS150 |
| B | LEU744 |
| site_id | BC1 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE FES B 4002 |
| Chain | Residue |
| B | GLY42 |
| B | CYS43 |
| B | GLY44 |
| B | GLY46 |
| B | GLY47 |
| B | CYS48 |
| B | GLY49 |
| B | CYS51 |
| B | ASN71 |
| B | CYS73 |
| site_id | BC2 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE MTE B 4003 |
| 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 | MOS4004 |
| B | HOH5063 |
| B | HOH5065 |
| B | HOH5104 |
| site_id | BC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MOS B 4004 |
| Chain | Residue |
| B | GLN767 |
| B | GLY799 |
| B | PHE911 |
| B | ARG912 |
| B | ALA1078 |
| B | ALA1079 |
| B | GLU1261 |
| B | MTE4003 |
| B | FYX4006 |
| site_id | BC4 |
| Number of Residues | 33 |
| Details | BINDING SITE FOR RESIDUE FAD B 4005 |
| Chain | Residue |
| B | GLU45 |
| B | GLY46 |
| 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 | ALA346 |
| B | SER347 |
| B | GLY350 |
| B | ASN351 |
| B | ILE353 |
| B | THR354 |
| B | SER359 |
| B | ASP360 |
| B | LEU404 |
| B | LYS422 |
| B | ASP429 |
| B | ASP430 |
| B | HOH5126 |
| B | HOH5191 |
| B | HOH5240 |
| B | HOH5252 |
| B | HOH5273 |
| B | HOH5474 |
| B | HOH5732 |
| site_id | BC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE FYX B 4006 |
| Chain | Residue |
| B | ASN768 |
| B | GLU802 |
| B | LEU873 |
| B | SER876 |
| B | ARG880 |
| B | PHE914 |
| B | PHE1009 |
| B | LEU1014 |
| B | PRO1076 |
| B | ALA1078 |
| B | ALA1079 |
| B | GLU1261 |
| B | MOS4004 |
| B | HOH5486 |
| B | HOH5497 |
| site_id | BC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ACY A 3007 |
| Chain | Residue |
| A | ARG839 |
| A | HIS840 |
| A | ILE877 |
| A | THR909 |
| A | ALA910 |
| A | PHE911 |
| A | PHE914 |
| A | GLY915 |
| A | GLN918 |
| site_id | BC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ACY B 4007 |
| Chain | Residue |
| B | ARG839 |
| B | HIS840 |
| B | ILE877 |
| B | THR909 |
| B | ALA910 |
| B | PHE911 |
| B | PHE914 |
| B | GLY915 |
| B | GLN918 |
| site_id | BC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 5001 |
| Chain | Residue |
| A | GLY664 |
| A | HIS665 |
| A | ILE666 |
| A | ARG804 |
| A | ASN869 |
| A | SER906 |
| A | SER907 |
| A | HOH5069 |
| A | HOH5801 |
| site_id | BC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 5002 |
| Chain | Residue |
| B | GLY664 |
| B | HIS665 |
| B | ILE666 |
| B | ARG804 |
| B | ASN869 |
| B | SER906 |
| B | SER907 |
| B | HOH5048 |
| B | HOH5889 |
| site_id | CC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 5003 |
| Chain | Residue |
| A | ASP594 |
| A | ARG824 |
| A | MET826 |
| A | HOH5160 |
| A | HOH5646 |
| A | HOH5885 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 5004 |
| Chain | Residue |
| B | ASP594 |
| B | PHE604 |
| B | ARG824 |
| B | MET826 |
| B | HOH5185 |
| B | HOH5510 |
| site_id | CC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 5005 |
| Chain | Residue |
| A | GLN561 |
| A | GLY574 |
| A | SER1184 |
| A | SER1185 |
| A | HOH5327 |
| A | HOH5694 |
| site_id | CC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 5006 |
| Chain | Residue |
| B | GLN561 |
| B | GLY574 |
| B | SER1184 |
| B | SER1185 |
| B | HOH5222 |
| B | HOH5288 |
| site_id | CC5 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE GOL A 5007 |
| Chain | Residue |
| A | GLN1088 |
| A | TYR1091 |
| A | TYR1254 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B 5008 |
| Chain | Residue |
| B | GLN1088 |
| B | TYR1091 |
| B | ILE1253 |
| B | TYR1254 |
| B | HOH5394 |
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 | 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 |
