1VDV
Bovine Milk Xanthine Dehydrogenase Y-700 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 5301 |
| 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 5302 |
| Chain | Residue |
| B | SER874 |
| B | SER907 |
| B | ASN908 |
| B | ALA867 |
| B | SER870 |
| B | ARG871 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 5303 |
| Chain | Residue |
| B | HIS741 |
| B | TYR743 |
| B | THR836 |
| B | GLY837 |
| B | HOH5367 |
| B | HOH6328 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 5304 |
| Chain | Residue |
| A | HIS741 |
| A | TYR743 |
| A | THR836 |
| A | GLY837 |
| A | HOH5508 |
| A | HOH6075 |
| site_id | AC5 |
| 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 | AC6 |
| Number of Residues | 9 |
| 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 | CYS73 |
| site_id | AC7 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE MTE A 3003 |
| Chain | Residue |
| A | GLN112 |
| A | CYS150 |
| A | GLY796 |
| A | GLY797 |
| A | PHE798 |
| A | ARG912 |
| A | MET1038 |
| A | GLY1039 |
| A | GLN1040 |
| A | ALA1078 |
| A | ALA1079 |
| A | SER1080 |
| A | VAL1081 |
| A | SER1082 |
| A | GLN1194 |
| A | MOS3004 |
| A | HOH5406 |
| A | HOH5427 |
| A | HOH5585 |
| site_id | AC8 |
| 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 | HOH5555 |
| site_id | AC9 |
| Number of Residues | 35 |
| Details | BINDING SITE FOR RESIDUE FAD A 3005 |
| Chain | Residue |
| A | HOH5577 |
| A | HOH5915 |
| A | HOH6017 |
| A | HOH6368 |
| 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 | GOL5004 |
| A | HOH5371 |
| site_id | BC1 |
| 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 | BC2 |
| Number of Residues | 9 |
| 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 | CYS73 |
| site_id | BC3 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE MTE B 4003 |
| Chain | Residue |
| B | GLN112 |
| B | CYS150 |
| B | GLY796 |
| B | GLY797 |
| B | PHE798 |
| B | ARG912 |
| B | MET1038 |
| B | GLY1039 |
| B | GLN1040 |
| B | ALA1078 |
| B | ALA1079 |
| B | SER1080 |
| B | VAL1081 |
| B | SER1082 |
| B | GLN1194 |
| B | MOS4004 |
| B | HOH5397 |
| B | HOH5456 |
| B | HOH5481 |
| site_id | BC4 |
| 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 | HOH6314 |
| site_id | BC5 |
| Number of Residues | 35 |
| Details | BINDING SITE FOR RESIDUE FAD B 4005 |
| Chain | Residue |
| B | GLU45 |
| B | GLY46 |
| B | GLY47 |
| 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 | GOL5021 |
| B | HOH5361 |
| B | HOH5706 |
| B | HOH5707 |
| B | HOH5771 |
| site_id | BC6 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE YSH A 5101 |
| Chain | Residue |
| A | ASN768 |
| A | GLU802 |
| A | LEU873 |
| A | SER876 |
| A | ARG880 |
| A | PHE914 |
| A | SER1008 |
| A | PHE1009 |
| A | THR1010 |
| A | VAL1011 |
| A | PHE1013 |
| A | LEU1014 |
| A | PRO1076 |
| A | ALA1079 |
| A | HOH5335 |
| A | HOH5555 |
| site_id | BC7 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE YSH B 5102 |
| Chain | Residue |
| B | ASN768 |
| B | GLU802 |
| B | LEU873 |
| B | SER876 |
| B | ARG880 |
| B | PHE914 |
| B | SER1008 |
| B | PHE1009 |
| B | THR1010 |
| B | VAL1011 |
| B | PHE1013 |
| B | LEU1014 |
| B | PRO1076 |
| B | ALA1079 |
| B | HOH5556 |
| B | HOH6314 |
| site_id | BC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 5001 |
| Chain | Residue |
| A | PHE549 |
| A | LYS994 |
| A | GLU1163 |
| A | ASP1170 |
| A | HIS1171 |
| A | LYS1172 |
| site_id | BC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL A 5002 |
| Chain | Residue |
| A | THR207 |
| A | LEU521 |
| A | LEU524 |
| A | LYS537 |
| A | LEU538 |
| A | ASP539 |
| A | HOH5542 |
| A | HOH5793 |
| A | HOH6040 |
| site_id | CC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 5003 |
| Chain | Residue |
| A | TRP336 |
| A | LYS422 |
| A | GLN423 |
| A | ARG427 |
| A | ASP1170 |
| A | HOH5603 |
| A | HOH5853 |
| site_id | CC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 5004 |
| Chain | Residue |
| A | GLU45 |
| A | ILE266 |
| A | SER1225 |
| A | FAD3005 |
| A | GOL5005 |
| A | HOH5710 |
| A | HOH6094 |
| site_id | CC3 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 5005 |
| Chain | Residue |
| A | GLU45 |
| A | ASN830 |
| A | ARG1222 |
| A | SER1225 |
| A | GOL5004 |
| A | HOH5506 |
| A | HOH6385 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 5006 |
| Chain | Residue |
| A | ASP594 |
| A | PHE604 |
| A | MET826 |
| A | HOH5429 |
| A | HOH5462 |
| site_id | CC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL B 5007 |
| Chain | Residue |
| B | THR207 |
| B | GLN208 |
| B | LEU524 |
| B | LYS537 |
| B | ASP539 |
| B | TYR542 |
| site_id | CC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 5008 |
| Chain | Residue |
| B | PHE549 |
| B | LYS994 |
| B | GLU1163 |
| B | ASP1170 |
| B | HIS1171 |
| B | LYS1172 |
| B | HOH6285 |
| site_id | CC7 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 5009 |
| Chain | Residue |
| B | TRP336 |
| B | LYS422 |
| B | GLN423 |
| B | ARG427 |
| B | ASP1170 |
| B | GOL5022 |
| B | HOH5487 |
| B | HOH5570 |
| B | HOH5644 |
| site_id | CC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL A 5011 |
| Chain | Residue |
| A | GLU759 |
| A | ASN785 |
| A | ARG786 |
| A | ILE787 |
| A | LEU788 |
| A | HOH5551 |
| B | LEU1030 |
| B | SER1064 |
| site_id | CC9 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 5012 |
| Chain | Residue |
| B | LEU580 |
| B | ALA581 |
| B | VAL1047 |
| B | TYR1062 |
| B | ILE1063 |
| B | HOH5461 |
| B | HOH5598 |
| B | HOH5735 |
| site_id | DC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 5013 |
| Chain | Residue |
| B | ARG31 |
| B | ARG37 |
| B | ASP594 |
| B | ASP595 |
| B | ILE596 |
| B | ARG824 |
| B | GOL5014 |
| B | HOH5396 |
| site_id | DC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL B 5014 |
| Chain | Residue |
| B | ASP594 |
| B | PHE604 |
| B | PRO675 |
| B | MET826 |
| B | GOL5013 |
| B | HOH5576 |
| B | HOH6239 |
| B | HOH6331 |
| site_id | DC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL B 5015 |
| Chain | Residue |
| B | HIS665 |
| B | ILE666 |
| B | ARG804 |
| B | ILE835 |
| B | ASN869 |
| B | SER906 |
| B | SER907 |
| B | HOH5767 |
| B | HOH6010 |
| site_id | DC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 5016 |
| Chain | Residue |
| A | LEU580 |
| A | ALA581 |
| A | VAL1047 |
| A | TYR1062 |
| A | ILE1063 |
| A | HOH5764 |
| site_id | DC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 5017 |
| Chain | Residue |
| A | GLN561 |
| A | GLY574 |
| A | SER1184 |
| A | SER1185 |
| A | HOH5490 |
| site_id | DC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL A 5018 |
| Chain | Residue |
| A | GLY664 |
| A | HIS665 |
| A | ILE666 |
| A | ARG804 |
| A | ILE835 |
| A | ASN869 |
| A | SER906 |
| A | SER907 |
| A | HOH5774 |
| A | HOH5951 |
| site_id | DC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL A 5019 |
| Chain | Residue |
| A | ARG606 |
| A | LEU607 |
| A | VAL608 |
| A | THR609 |
| A | HIS683 |
| A | HOH5564 |
| A | HOH5998 |
| site_id | DC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL B 5020 |
| Chain | Residue |
| B | GLU45 |
| B | ILE266 |
| B | LYS271 |
| B | GOL5021 |
| site_id | DC9 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL B 5021 |
| Chain | Residue |
| B | ILE266 |
| B | SER1225 |
| B | FAD4005 |
| B | GOL5020 |
| B | HOH5634 |
| site_id | EC1 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL B 5022 |
| Chain | Residue |
| B | GLU332 |
| B | PHE421 |
| B | LYS518 |
| B | LEU548 |
| B | PHE549 |
| B | GOL5009 |
| B | HOH5457 |
| site_id | EC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ACY A 5201 |
| Chain | Residue |
| A | ARG839 |
| A | HIS840 |
| A | ILE877 |
| A | THR909 |
| A | ALA910 |
| A | PHE911 |
| A | PHE914 |
| A | GLY915 |
| A | GLN918 |
| site_id | EC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE ACY B 5202 |
| 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 | 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 |
