1KY4
S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0001666 | biological_process | response to hypoxia |
A | 0002439 | biological_process | chronic inflammatory response to antigenic stimulus |
A | 0004013 | molecular_function | adenosylhomocysteinase activity |
A | 0005507 | molecular_function | copper ion binding |
A | 0005634 | cellular_component | nucleus |
A | 0005737 | cellular_component | cytoplasm |
A | 0005783 | cellular_component | endoplasmic reticulum |
A | 0005829 | cellular_component | cytosol |
A | 0006730 | biological_process | one-carbon metabolic process |
A | 0007584 | biological_process | response to nutrient |
A | 0016787 | molecular_function | hydrolase activity |
A | 0019510 | biological_process | S-adenosylhomocysteine catabolic process |
A | 0030554 | molecular_function | adenyl nucleotide binding |
A | 0033353 | biological_process | S-adenosylmethionine cycle |
A | 0042470 | cellular_component | melanosome |
A | 0042745 | biological_process | circadian sleep/wake cycle |
A | 0042802 | molecular_function | identical protein binding |
A | 0051287 | molecular_function | NAD binding |
A | 0098604 | molecular_function | adenosylselenohomocysteinase activity |
B | 0001666 | biological_process | response to hypoxia |
B | 0002439 | biological_process | chronic inflammatory response to antigenic stimulus |
B | 0004013 | molecular_function | adenosylhomocysteinase activity |
B | 0005507 | molecular_function | copper ion binding |
B | 0005634 | cellular_component | nucleus |
B | 0005737 | cellular_component | cytoplasm |
B | 0005783 | cellular_component | endoplasmic reticulum |
B | 0005829 | cellular_component | cytosol |
B | 0006730 | biological_process | one-carbon metabolic process |
B | 0007584 | biological_process | response to nutrient |
B | 0016787 | molecular_function | hydrolase activity |
B | 0019510 | biological_process | S-adenosylhomocysteine catabolic process |
B | 0030554 | molecular_function | adenyl nucleotide binding |
B | 0033353 | biological_process | S-adenosylmethionine cycle |
B | 0042470 | cellular_component | melanosome |
B | 0042745 | biological_process | circadian sleep/wake cycle |
B | 0042802 | molecular_function | identical protein binding |
B | 0051287 | molecular_function | NAD binding |
B | 0098604 | molecular_function | adenosylselenohomocysteinase activity |
C | 0001666 | biological_process | response to hypoxia |
C | 0002439 | biological_process | chronic inflammatory response to antigenic stimulus |
C | 0004013 | molecular_function | adenosylhomocysteinase activity |
C | 0005507 | molecular_function | copper ion binding |
C | 0005634 | cellular_component | nucleus |
C | 0005737 | cellular_component | cytoplasm |
C | 0005783 | cellular_component | endoplasmic reticulum |
C | 0005829 | cellular_component | cytosol |
C | 0006730 | biological_process | one-carbon metabolic process |
C | 0007584 | biological_process | response to nutrient |
C | 0016787 | molecular_function | hydrolase activity |
C | 0019510 | biological_process | S-adenosylhomocysteine catabolic process |
C | 0030554 | molecular_function | adenyl nucleotide binding |
C | 0033353 | biological_process | S-adenosylmethionine cycle |
C | 0042470 | cellular_component | melanosome |
C | 0042745 | biological_process | circadian sleep/wake cycle |
C | 0042802 | molecular_function | identical protein binding |
C | 0051287 | molecular_function | NAD binding |
C | 0098604 | molecular_function | adenosylselenohomocysteinase activity |
D | 0001666 | biological_process | response to hypoxia |
D | 0002439 | biological_process | chronic inflammatory response to antigenic stimulus |
D | 0004013 | molecular_function | adenosylhomocysteinase activity |
D | 0005507 | molecular_function | copper ion binding |
D | 0005634 | cellular_component | nucleus |
D | 0005737 | cellular_component | cytoplasm |
D | 0005783 | cellular_component | endoplasmic reticulum |
D | 0005829 | cellular_component | cytosol |
D | 0006730 | biological_process | one-carbon metabolic process |
D | 0007584 | biological_process | response to nutrient |
D | 0016787 | molecular_function | hydrolase activity |
D | 0019510 | biological_process | S-adenosylhomocysteine catabolic process |
D | 0030554 | molecular_function | adenyl nucleotide binding |
D | 0033353 | biological_process | S-adenosylmethionine cycle |
D | 0042470 | cellular_component | melanosome |
D | 0042745 | biological_process | circadian sleep/wake cycle |
D | 0042802 | molecular_function | identical protein binding |
D | 0051287 | molecular_function | NAD binding |
D | 0098604 | molecular_function | adenosylselenohomocysteinase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE NAD A 432 |
Chain | Residue |
A | ASP189 |
A | ASP244 |
A | ASN247 |
A | THR274 |
A | THR275 |
A | GLY276 |
A | ILE280 |
A | ILE298 |
A | GLY299 |
A | HIS300 |
A | LEU343 |
A | ASN190 |
A | ASN345 |
A | HIS352 |
A | HOH5040 |
A | HOH5337 |
B | GLN1412 |
B | LYS1425 |
B | TYR1429 |
A | GLY219 |
A | GLY221 |
A | ASP222 |
A | VAL223 |
A | THR241 |
A | GLU242 |
A | ILE243 |
site_id | AC2 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE NAD B 1432 |
Chain | Residue |
A | GLN412 |
A | LYS425 |
A | TYR429 |
B | ASP1189 |
B | ASN1190 |
B | GLY1219 |
B | GLY1221 |
B | ASP1222 |
B | VAL1223 |
B | THR1241 |
B | GLU1242 |
B | ILE1243 |
B | ASP1244 |
B | ASN1247 |
B | THR1274 |
B | THR1275 |
B | GLY1276 |
B | ILE1280 |
B | ILE1298 |
B | GLY1299 |
B | HIS1300 |
B | LEU1343 |
B | ASN1345 |
B | HIS1352 |
B | HOH5125 |
B | HOH5145 |
site_id | AC3 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE NAD C 2432 |
Chain | Residue |
C | ASP2189 |
C | ASN2190 |
C | GLY2219 |
C | GLY2221 |
C | ASP2222 |
C | VAL2223 |
C | THR2241 |
C | GLU2242 |
C | ILE2243 |
C | ASP2244 |
C | ASN2247 |
C | THR2274 |
C | THR2275 |
C | GLY2276 |
C | ILE2280 |
C | ILE2298 |
C | GLY2299 |
C | HIS2300 |
C | LEU2343 |
C | ASN2345 |
C | HIS2352 |
C | HOH5041 |
D | GLN3412 |
D | LYS3425 |
D | TYR3429 |
site_id | AC4 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE NAD D 3432 |
Chain | Residue |
D | ASN3345 |
D | HIS3352 |
D | HOH5216 |
C | GLN2412 |
C | LYS2425 |
C | TYR2429 |
D | ASP3189 |
D | ASN3190 |
D | GLY3219 |
D | GLY3221 |
D | ASP3222 |
D | VAL3223 |
D | THR3241 |
D | GLU3242 |
D | ILE3243 |
D | ASP3244 |
D | ASN3247 |
D | THR3274 |
D | THR3275 |
D | GLY3276 |
D | ILE3280 |
D | ILE3298 |
D | GLY3299 |
D | HIS3300 |
D | LEU3343 |
Functional Information from PROSITE/UniProt
site_id | PS00738 |
Number of Residues | 15 |
Details | ADOHCYASE_1 S-adenosyl-L-homocysteine hydrolase signature 1. SCNiFSTQDhAAAAI |
Chain | Residue | Details |
A | SER77-ILE91 |
site_id | PS00739 |
Number of Residues | 17 |
Details | ADOHCYASE_2 S-adenosyl-L-homocysteine hydrolase signature 2. GKvavVaGYGdVGKGc.A |
Chain | Residue | Details |
A | GLY212-ALA228 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11741948 |
Chain | Residue | Details |
A | VAL57 | |
A | THR156 | |
B | VAL1057 | |
B | THR1156 | |
C | VAL2057 | |
C | THR2156 | |
D | VAL3057 | |
D | THR3156 |
site_id | SWS_FT_FI2 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11927587 |
Chain | Residue | Details |
A | GLY131 | |
B | GLY1131 | |
C | GLY2131 | |
D | GLY3131 |
site_id | SWS_FT_FI3 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10913437, ECO:0000269|PubMed:11741948, ECO:0000269|PubMed:11927587, ECO:0007744|PDB:1D4F, ECO:0007744|PDB:1K0U, ECO:0007744|PDB:1KY5, ECO:0007744|PDB:2H5L |
Chain | Residue | Details |
A | THR157 | |
B | THR1157 | |
C | THR2157 | |
D | THR3157 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:11741948, ECO:0000269|PubMed:11927587 |
Chain | Residue | Details |
A | SER186 | |
A | ASN190 | |
B | SER1186 | |
B | ASN1190 | |
C | SER2186 | |
C | ASN2190 | |
D | SER3186 | |
D | ASN3190 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10387078 |
Chain | Residue | Details |
A | ASP222 | |
A | ILE243 | |
B | ASP1222 | |
B | ILE1243 | |
C | ASP2222 | |
C | ILE2243 | |
D | ASP3222 | |
D | ILE3243 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10913437, ECO:0000269|PubMed:11741948, ECO:0000269|PubMed:11927587, ECO:0007744|PDB:1D4F, ECO:0007744|PDB:1K0U, ECO:0007744|PDB:1KY4, ECO:0007744|PDB:1XWF, ECO:0007744|PDB:2H5L |
Chain | Residue | Details |
A | ALA248 | |
B | ALA1248 | |
C | ALA2248 | |
D | ALA3248 |
site_id | SWS_FT_FI7 |
Number of Residues | 12 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10387078, ECO:0000269|PubMed:10913437, ECO:0000269|PubMed:11741948, ECO:0000269|PubMed:11927587, ECO:0007744|PDB:1B3R, ECO:0007744|PDB:1D4F, ECO:0007744|PDB:1K0U, ECO:0007744|PDB:1KY4, ECO:0007744|PDB:1KY5, ECO:0007744|PDB:1XWF, ECO:0007744|PDB:2H5L |
Chain | Residue | Details |
A | GLY299 | |
D | GLY3299 | |
D | LEU3346 | |
D | ARG3430 | |
A | LEU346 | |
A | ARG430 | |
B | GLY1299 | |
B | LEU1346 | |
B | ARG1430 | |
C | GLY2299 | |
C | LEU2346 | |
C | ARG2430 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10387078, ECO:0000269|PubMed:10913437, ECO:0000269|PubMed:11741948, ECO:0007744|PDB:1B3R, ECO:0007744|PDB:1D4F, ECO:0007744|PDB:1K0U, ECO:0007744|PDB:1XWF, ECO:0007744|PDB:2H5L |
Chain | Residue | Details |
A | PRO353 | |
B | PRO1353 | |
C | PRO2353 | |
D | PRO3353 |
site_id | SWS_FT_FI9 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:10387078, ECO:0000269|PubMed:11741948, ECO:0000269|PubMed:11927587, ECO:0007744|PDB:1B3R, ECO:0007744|PDB:1K0U, ECO:0007744|PDB:1KY4, ECO:0007744|PDB:1KY5, ECO:0007744|PDB:1XWF, ECO:0007744|PDB:2H5L |
Chain | Residue | Details |
A | PRO426 | |
B | PRO1426 | |
C | PRO2426 | |
D | PRO3426 |
site_id | SWS_FT_FI10 |
Number of Residues | 4 |
Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P23526 |
Chain | Residue | Details |
A | VAL183 | |
B | VAL1183 | |
C | VAL2183 | |
D | VAL3183 |
site_id | SWS_FT_FI11 |
Number of Residues | 4 |
Details | MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000250|UniProtKB:P23526 |
Chain | Residue | Details |
A | SER186 | |
B | SER1186 | |
C | SER2186 | |
D | SER3186 |
site_id | SWS_FT_FI12 |
Number of Residues | 4 |
Details | MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P50247 |
Chain | Residue | Details |
A | GLY193 | |
B | GLY1193 | |
C | GLY2193 | |
D | GLY3193 |
Catalytic Information from CSA
site_id | CSA1 |
Number of Residues | 7 |
Details | Annotated By Reference To The Literature 1b3r |
Chain | Residue | Details |
A | HIS54 | |
A | LYS185 | |
A | ASP189 | |
A | HIS300 | |
A | ASP130 | |
A | CYS194 | |
A | ASN190 |
site_id | CSA2 |
Number of Residues | 7 |
Details | Annotated By Reference To The Literature 1b3r |
Chain | Residue | Details |
B | ASP1189 | |
B | CYS1194 | |
B | ASN1190 | |
B | HIS1300 | |
B | ASP1130 | |
B | LYS1185 | |
B | HIS1054 |
site_id | CSA3 |
Number of Residues | 7 |
Details | Annotated By Reference To The Literature 1b3r |
Chain | Residue | Details |
C | LYS2185 | |
C | HIS2054 | |
C | ASN2190 | |
C | ASP2130 | |
C | ASP2189 | |
C | HIS2300 | |
C | CYS2194 |
site_id | CSA4 |
Number of Residues | 7 |
Details | Annotated By Reference To The Literature 1b3r |
Chain | Residue | Details |
D | HIS3054 | |
D | ASN3190 | |
D | ASP3189 | |
D | HIS3300 | |
D | CYS3194 | |
D | ASP3130 | |
D | LYS3185 |
site_id | MCSA1 |
Number of Residues | 14 |
Details | M-CSA 90 |
Chain | Residue | Details |
A | MET55 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
A | ARG195 | electrostatic stabiliser, polar/non-polar interaction |
A | PHE301 | activator, electrostatic stabiliser, hydrogen bond acceptor |
A | PRO353 | electrostatic stabiliser |
A | PHE361 | electrostatic stabiliser, hydrogen bond donor |
A | VAL365 | activator, electrostatic stabiliser |
A | CYS78 | electrostatic stabiliser |
A | THR83 | electrostatic stabiliser |
A | GLY131 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
A | THR156 | electrostatic stabiliser, proton acceptor, proton donor |
A | ASP181 | activator, electrostatic stabiliser |
A | SER186 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
A | ASN190 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
A | LEU191 | electrostatic stabiliser, hydrogen bond acceptor |
site_id | MCSA2 |
Number of Residues | 14 |
Details | M-CSA 90 |
Chain | Residue | Details |
B | MET1055 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
B | ARG1195 | electrostatic stabiliser, polar/non-polar interaction |
B | PHE1301 | activator, electrostatic stabiliser, hydrogen bond acceptor |
B | PRO1353 | electrostatic stabiliser |
B | PHE1361 | electrostatic stabiliser, hydrogen bond donor |
B | VAL1365 | activator, electrostatic stabiliser |
B | CYS1078 | electrostatic stabiliser |
B | THR1083 | electrostatic stabiliser |
B | GLY1131 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
B | THR1156 | electrostatic stabiliser, proton acceptor, proton donor |
B | ASP1181 | activator, electrostatic stabiliser |
B | SER1186 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
B | ASN1190 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
B | LEU1191 | electrostatic stabiliser, hydrogen bond acceptor |
site_id | MCSA3 |
Number of Residues | 14 |
Details | M-CSA 90 |
Chain | Residue | Details |
C | MET2055 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
C | ARG2195 | electrostatic stabiliser, polar/non-polar interaction |
C | PHE2301 | activator, electrostatic stabiliser, hydrogen bond acceptor |
C | PRO2353 | electrostatic stabiliser |
C | PHE2361 | electrostatic stabiliser, hydrogen bond donor |
C | VAL2365 | activator, electrostatic stabiliser |
C | CYS2078 | electrostatic stabiliser |
C | THR2083 | electrostatic stabiliser |
C | GLY2131 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
C | THR2156 | electrostatic stabiliser, proton acceptor, proton donor |
C | ASP2181 | activator, electrostatic stabiliser |
C | SER2186 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
C | ASN2190 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
C | LEU2191 | electrostatic stabiliser, hydrogen bond acceptor |
site_id | MCSA4 |
Number of Residues | 14 |
Details | M-CSA 90 |
Chain | Residue | Details |
D | MET3055 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
D | ARG3195 | electrostatic stabiliser, polar/non-polar interaction |
D | PHE3301 | activator, electrostatic stabiliser, hydrogen bond acceptor |
D | PRO3353 | electrostatic stabiliser |
D | PHE3361 | electrostatic stabiliser, hydrogen bond donor |
D | VAL3365 | activator, electrostatic stabiliser |
D | CYS3078 | electrostatic stabiliser |
D | THR3083 | electrostatic stabiliser |
D | GLY3131 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
D | THR3156 | electrostatic stabiliser, proton acceptor, proton donor |
D | ASP3181 | activator, electrostatic stabiliser |
D | SER3186 | electrostatic stabiliser, hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor |
D | ASN3190 | electrostatic stabiliser, hydrogen bond acceptor, proton acceptor, proton donor |
D | LEU3191 | electrostatic stabiliser, hydrogen bond acceptor |