1SDY
STRUCTURE SOLUTION AND MOLECULAR DYNAMICS REFINEMENT OF THE YEAST CU,ZN ENZYME SUPEROXIDE DISMUTASE
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0004784 | molecular_function | superoxide dismutase activity |
| A | 0005507 | molecular_function | copper ion binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005634 | cellular_component | nucleus |
| A | 0005737 | cellular_component | cytoplasm |
| A | 0005739 | cellular_component | mitochondrion |
| A | 0005758 | cellular_component | mitochondrial intermembrane space |
| A | 0005829 | cellular_component | cytosol |
| A | 0006801 | biological_process | superoxide metabolic process |
| A | 0006878 | biological_process | intracellular copper ion homeostasis |
| A | 0006882 | biological_process | intracellular zinc ion homeostasis |
| A | 0008270 | molecular_function | zinc ion binding |
| A | 0015680 | biological_process | protein maturation by copper ion transfer |
| A | 0016209 | molecular_function | antioxidant activity |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0016670 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor |
| A | 0019430 | biological_process | removal of superoxide radicals |
| A | 0031505 | biological_process | fungal-type cell wall organization |
| A | 0034599 | biological_process | cellular response to oxidative stress |
| A | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| A | 0046872 | molecular_function | metal ion binding |
| A | 0050821 | biological_process | protein stabilization |
| A | 1901856 | biological_process | negative regulation of cellular respiration |
| A | 1902693 | cellular_component | superoxide dismutase complex |
| A | 1990748 | biological_process | cellular detoxification |
| B | 0004784 | molecular_function | superoxide dismutase activity |
| B | 0005507 | molecular_function | copper ion binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005634 | cellular_component | nucleus |
| B | 0005737 | cellular_component | cytoplasm |
| B | 0005739 | cellular_component | mitochondrion |
| B | 0005758 | cellular_component | mitochondrial intermembrane space |
| B | 0005829 | cellular_component | cytosol |
| B | 0006801 | biological_process | superoxide metabolic process |
| B | 0006878 | biological_process | intracellular copper ion homeostasis |
| B | 0006882 | biological_process | intracellular zinc ion homeostasis |
| B | 0008270 | molecular_function | zinc ion binding |
| B | 0015680 | biological_process | protein maturation by copper ion transfer |
| B | 0016209 | molecular_function | antioxidant activity |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0016670 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor |
| B | 0019430 | biological_process | removal of superoxide radicals |
| B | 0031505 | biological_process | fungal-type cell wall organization |
| B | 0034599 | biological_process | cellular response to oxidative stress |
| B | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0050821 | biological_process | protein stabilization |
| B | 1901856 | biological_process | negative regulation of cellular respiration |
| B | 1902693 | cellular_component | superoxide dismutase complex |
| B | 1990748 | biological_process | cellular detoxification |
| C | 0004784 | molecular_function | superoxide dismutase activity |
| C | 0005507 | molecular_function | copper ion binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005737 | cellular_component | cytoplasm |
| C | 0005739 | cellular_component | mitochondrion |
| C | 0005758 | cellular_component | mitochondrial intermembrane space |
| C | 0005829 | cellular_component | cytosol |
| C | 0006801 | biological_process | superoxide metabolic process |
| C | 0006878 | biological_process | intracellular copper ion homeostasis |
| C | 0006882 | biological_process | intracellular zinc ion homeostasis |
| C | 0008270 | molecular_function | zinc ion binding |
| C | 0015680 | biological_process | protein maturation by copper ion transfer |
| C | 0016209 | molecular_function | antioxidant activity |
| C | 0016491 | molecular_function | oxidoreductase activity |
| C | 0016670 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor |
| C | 0019430 | biological_process | removal of superoxide radicals |
| C | 0031505 | biological_process | fungal-type cell wall organization |
| C | 0034599 | biological_process | cellular response to oxidative stress |
| C | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| C | 0046872 | molecular_function | metal ion binding |
| C | 0050821 | biological_process | protein stabilization |
| C | 1901856 | biological_process | negative regulation of cellular respiration |
| C | 1902693 | cellular_component | superoxide dismutase complex |
| C | 1990748 | biological_process | cellular detoxification |
| D | 0004784 | molecular_function | superoxide dismutase activity |
| D | 0005507 | molecular_function | copper ion binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005634 | cellular_component | nucleus |
| D | 0005737 | cellular_component | cytoplasm |
| D | 0005739 | cellular_component | mitochondrion |
| D | 0005758 | cellular_component | mitochondrial intermembrane space |
| D | 0005829 | cellular_component | cytosol |
| D | 0006801 | biological_process | superoxide metabolic process |
| D | 0006878 | biological_process | intracellular copper ion homeostasis |
| D | 0006882 | biological_process | intracellular zinc ion homeostasis |
| D | 0008270 | molecular_function | zinc ion binding |
| D | 0015680 | biological_process | protein maturation by copper ion transfer |
| D | 0016209 | molecular_function | antioxidant activity |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0016670 | molecular_function | oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor |
| D | 0019430 | biological_process | removal of superoxide radicals |
| D | 0031505 | biological_process | fungal-type cell wall organization |
| D | 0034599 | biological_process | cellular response to oxidative stress |
| D | 0045944 | biological_process | positive regulation of transcription by RNA polymerase II |
| D | 0046872 | molecular_function | metal ion binding |
| D | 0050821 | biological_process | protein stabilization |
| D | 1901856 | biological_process | negative regulation of cellular respiration |
| D | 1902693 | cellular_component | superoxide dismutase complex |
| D | 1990748 | biological_process | cellular detoxification |
Functional Information from PDB Data
| site_id | A |
| Number of Residues | 9 |
| Details |
| Chain | Residue |
| A | HIS44 |
| A | HIS46 |
| A | HIS61 |
| A | HIS118 |
| A | HIS69 |
| A | HIS78 |
| A | ASP81 |
| A | CU152 |
| A | ZN153 |
| site_id | AC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CU A 152 |
| Chain | Residue |
| A | HIS44 |
| A | HIS46 |
| A | HIS61 |
| A | HIS118 |
| A | HOH154 |
| site_id | AC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN A 153 |
| Chain | Residue |
| A | HIS61 |
| A | HIS69 |
| A | HIS78 |
| A | ASP81 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CU B 152 |
| Chain | Residue |
| B | HIS44 |
| B | HIS46 |
| B | HIS61 |
| B | HIS118 |
| B | HOH154 |
| site_id | AC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN B 153 |
| Chain | Residue |
| B | HIS61 |
| B | HIS69 |
| B | HIS78 |
| B | ASP81 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CU C 152 |
| Chain | Residue |
| C | HIS44 |
| C | HIS46 |
| C | HIS61 |
| C | HIS118 |
| C | HOH154 |
| site_id | AC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN C 153 |
| Chain | Residue |
| C | HIS61 |
| C | HIS69 |
| C | HIS78 |
| C | ASP81 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CU D 152 |
| Chain | Residue |
| D | HIS44 |
| D | HIS46 |
| D | HIS61 |
| D | HIS118 |
| D | HOH154 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE ZN D 153 |
| Chain | Residue |
| D | HIS61 |
| D | HIS69 |
| D | HIS78 |
| D | ASP81 |
| site_id | B |
| Number of Residues | 9 |
| Details |
| Chain | Residue |
| B | HIS44 |
| B | HIS46 |
| B | HIS61 |
| B | HIS118 |
| B | HIS69 |
| B | HIS78 |
| B | ASP81 |
| B | CU152 |
| B | ZN153 |
| site_id | C |
| Number of Residues | 9 |
| Details |
| Chain | Residue |
| C | HIS44 |
| C | HIS46 |
| C | HIS61 |
| C | HIS118 |
| C | HIS69 |
| C | HIS78 |
| C | ASP81 |
| C | CU152 |
| C | ZN153 |
| site_id | D |
| Number of Residues | 9 |
| Details |
| Chain | Residue |
| D | HIS44 |
| D | HIS46 |
| D | HIS61 |
| D | HIS118 |
| D | HIS69 |
| D | HIS78 |
| D | ASP81 |
| D | CU152 |
| D | ZN153 |
Functional Information from PROSITE/UniProt
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 4 |
| Details | BINDING: in apo form => ECO:0000269|PubMed:10026301, ECO:0000269|PubMed:11524675 |
| Chain | Residue | Details |
| A | ARG41 | |
| B | ARG41 | |
| C | ARG41 | |
| D | ARG41 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 12 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10026301, ECO:0000269|PubMed:8652572 |
| Chain | Residue | Details |
| A | ILE45 | |
| D | ILE45 | |
| D | GLU47 | |
| D | ALA119 | |
| A | GLU47 | |
| A | ALA119 | |
| B | ILE45 | |
| B | GLU47 | |
| B | ALA119 | |
| C | ILE45 | |
| C | GLU47 | |
| C | ALA119 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 16 |
| Details | BINDING: BINDING => ECO:0000269|PubMed:10026301, ECO:0000269|PubMed:11524675 |
| Chain | Residue | Details |
| A | PHE62 | |
| C | GLY70 | |
| C | VAL79 | |
| C | MET82 | |
| D | PHE62 | |
| D | GLY70 | |
| D | VAL79 | |
| D | MET82 | |
| A | GLY70 | |
| A | VAL79 | |
| A | MET82 | |
| B | PHE62 | |
| B | GLY70 | |
| B | VAL79 | |
| B | MET82 | |
| C | PHE62 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 4 |
| Details | BINDING: BINDING => ECO:0000305 |
| Chain | Residue | Details |
| A | PRO142 | |
| B | PRO142 | |
| C | PRO142 | |
| D | PRO142 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18407956 |
| Chain | Residue | Details |
| A | GLU25 | |
| B | GLU25 | |
| C | GLU25 | |
| D | GLU25 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:15665377, ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| A | PRO37 | |
| B | PRO37 | |
| C | PRO37 | |
| D | PRO37 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17287358, ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| A | PHE97 | |
| B | PHE97 | |
| C | PHE97 | |
| D | PHE97 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17287358 |
| Chain | Residue | Details |
| A | VAL115 | |
| B | VAL115 | |
| C | VAL115 | |
| D | VAL115 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17287358 |
| Chain | Residue | Details |
| A | GLU130 | |
| B | GLU130 | |
| C | GLU130 | |
| D | GLU130 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 4 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19779198 |
| Chain | Residue | Details |
| A | GLY136 | |
| B | GLY136 | |
| C | GLY136 | |
| D | GLY136 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 12 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO) => ECO:0000269|PubMed:15166219 |
| Chain | Residue | Details |
| A | PHE20 | |
| D | PHE20 | |
| D | THR68 | |
| A | THR68 | |
| B | PHE20 | |
| B | THR68 | |
| C | PHE20 | |
| C | THR68 |
Catalytic Information from CSA
| site_id | CSA1 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| A | HIS61 | |
| A | ARG141 |
| site_id | CSA2 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| B | HIS61 | |
| B | ARG141 |
| site_id | CSA3 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| C | HIS61 | |
| C | ARG141 |
| site_id | CSA4 |
| Number of Residues | 2 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| D | HIS61 | |
| D | ARG141 |
| site_id | CSA5 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| A | HIS61 |
| site_id | CSA6 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| B | HIS61 |
| site_id | CSA7 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| C | HIS61 |
| site_id | CSA8 |
| Number of Residues | 1 |
| Details | Annotated By Reference To The Literature 2jcw |
| Chain | Residue | Details |
| D | HIS61 |
| site_id | MCSA1 |
| Number of Residues | 8 |
| Details | M-CSA 138 |
| Chain | Residue | Details |
| A | ILE45 | metal ligand |
| A | GLU47 | metal ligand |
| A | PHE62 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
| A | GLY70 | metal ligand |
| A | VAL79 | metal ligand |
| A | MET82 | metal ligand |
| A | ALA119 | metal ligand |
| A | PRO142 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA2 |
| Number of Residues | 8 |
| Details | M-CSA 138 |
| Chain | Residue | Details |
| B | ILE45 | metal ligand |
| B | GLU47 | metal ligand |
| B | PHE62 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
| B | GLY70 | metal ligand |
| B | VAL79 | metal ligand |
| B | MET82 | metal ligand |
| B | ALA119 | metal ligand |
| B | PRO142 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA3 |
| Number of Residues | 8 |
| Details | M-CSA 138 |
| Chain | Residue | Details |
| C | ILE45 | metal ligand |
| C | GLU47 | metal ligand |
| C | PHE62 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
| C | GLY70 | metal ligand |
| C | VAL79 | metal ligand |
| C | MET82 | metal ligand |
| C | ALA119 | metal ligand |
| C | PRO142 | electrostatic stabiliser, hydrogen bond donor |
| site_id | MCSA4 |
| Number of Residues | 8 |
| Details | M-CSA 138 |
| Chain | Residue | Details |
| D | ILE45 | metal ligand |
| D | GLU47 | metal ligand |
| D | PHE62 | hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor |
| D | GLY70 | metal ligand |
| D | VAL79 | metal ligand |
| D | MET82 | metal ligand |
| D | ALA119 | metal ligand |
| D | PRO142 | electrostatic stabiliser, hydrogen bond donor |
