6XXI
Crystal Structure of Human Deoxyhypusine Synthase in complex with NAD
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005515 | molecular_function | protein binding |
A | 0005737 | cellular_component | cytoplasm |
A | 0005829 | cellular_component | cytosol |
A | 0006412 | biological_process | translation |
A | 0008216 | biological_process | spermidine metabolic process |
A | 0008284 | biological_process | positive regulation of cell population proliferation |
A | 0008612 | biological_process | peptidyl-lysine modification to peptidyl-hypusine |
A | 0016740 | molecular_function | transferase activity |
A | 0034038 | molecular_function | deoxyhypusine synthase activity |
A | 0042102 | biological_process | positive regulation of T cell proliferation |
A | 0042593 | biological_process | glucose homeostasis |
A | 0042802 | molecular_function | identical protein binding |
A | 0046203 | biological_process | spermidine catabolic process |
B | 0005515 | molecular_function | protein binding |
B | 0005737 | cellular_component | cytoplasm |
B | 0005829 | cellular_component | cytosol |
B | 0006412 | biological_process | translation |
B | 0008216 | biological_process | spermidine metabolic process |
B | 0008284 | biological_process | positive regulation of cell population proliferation |
B | 0008612 | biological_process | peptidyl-lysine modification to peptidyl-hypusine |
B | 0016740 | molecular_function | transferase activity |
B | 0034038 | molecular_function | deoxyhypusine synthase activity |
B | 0042102 | biological_process | positive regulation of T cell proliferation |
B | 0042593 | biological_process | glucose homeostasis |
B | 0042802 | molecular_function | identical protein binding |
B | 0046203 | biological_process | spermidine catabolic process |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 5 |
Details | binding site for residue ACT A 1101 |
Chain | Residue |
A | LYS141 |
A | LEU143 |
A | ALA144 |
A | PRO145 |
A | HOH1338 |
site_id | AC2 |
Number of Residues | 3 |
Details | binding site for residue EDO A 1102 |
Chain | Residue |
A | ASN37 |
B | GLN121 |
B | PRO217 |
site_id | AC3 |
Number of Residues | 1 |
Details | binding site for residue ACT A 1104 |
Chain | Residue |
A | HOH1269 |
site_id | AC4 |
Number of Residues | 29 |
Details | binding site for residue NAD A 1105 |
Chain | Residue |
A | THR104 |
A | SER105 |
A | ASN106 |
A | SER109 |
A | THR131 |
A | ALA132 |
A | GLY133 |
A | GLU136 |
A | GLU137 |
A | ASP238 |
A | GLY282 |
A | GLY283 |
A | ASN307 |
A | THR308 |
A | ALA309 |
A | SER317 |
A | ALA341 |
A | ASP342 |
A | ALA343 |
A | HOH1204 |
A | HOH1273 |
B | GLY284 |
B | VAL285 |
B | HIS288 |
B | ASP313 |
B | SER315 |
B | ASP316 |
B | SER317 |
B | EDO1518 |
site_id | AC5 |
Number of Residues | 6 |
Details | binding site for residue BME A 1106 |
Chain | Residue |
A | LEU87 |
A | GLU261 |
A | ARG264 |
A | LEU265 |
A | THR268 |
B | TYR250 |
site_id | AC6 |
Number of Residues | 3 |
Details | binding site for residue BME A 1107 |
Chain | Residue |
A | GLU180 |
A | PHE247 |
A | HOH1373 |
site_id | AC7 |
Number of Residues | 3 |
Details | binding site for residue BME A 1108 |
Chain | Residue |
A | TYR176 |
A | SER240 |
A | ASP243 |
site_id | AC8 |
Number of Residues | 4 |
Details | binding site for residue ACT A 1109 |
Chain | Residue |
A | ASN41 |
A | MET184 |
A | LYS251 |
A | HOH1292 |
site_id | AC9 |
Number of Residues | 1 |
Details | binding site for residue ACT A 1110 |
Chain | Residue |
B | SER28 |
site_id | AD1 |
Number of Residues | 5 |
Details | binding site for residue ACT A 1111 |
Chain | Residue |
A | CYS142 |
A | LEU143 |
A | ILE214 |
A | ASN216 |
A | HOH1297 |
site_id | AD2 |
Number of Residues | 8 |
Details | binding site for residue EDO A 1113 |
Chain | Residue |
A | ALA224 |
A | GLN225 |
A | HIS228 |
A | ILE229 |
A | PRO230 |
A | HOH1206 |
A | HOH1208 |
A | HOH1210 |
site_id | AD3 |
Number of Residues | 5 |
Details | binding site for residue EDO A 1114 |
Chain | Residue |
A | ARG320 |
A | ASP322 |
A | HOH1223 |
A | HOH1226 |
B | SER152 |
site_id | AD4 |
Number of Residues | 6 |
Details | binding site for residue EDO A 1115 |
Chain | Residue |
A | GLY33 |
A | ARG38 |
A | ALA48 |
A | THR51 |
A | HOH1258 |
A | HOH1293 |
site_id | AD5 |
Number of Residues | 4 |
Details | binding site for residue EDO A 1116 |
Chain | Residue |
A | ALA68 |
A | GLU71 |
A | LYS72 |
A | TYR302 |
site_id | AD6 |
Number of Residues | 4 |
Details | binding site for residue EDO A 1117 |
Chain | Residue |
A | ASN195 |
A | HOH1239 |
B | ALA356 |
B | HOH1682 |
site_id | AD7 |
Number of Residues | 7 |
Details | binding site for residue EDO A 1118 |
Chain | Residue |
A | HIS288 |
A | TRP327 |
A | LYS329 |
B | GLY239 |
B | SER240 |
B | NAD1510 |
B | HOH1611 |
site_id | AD8 |
Number of Residues | 4 |
Details | binding site for residue EDO A 1119 |
Chain | Residue |
A | ALA144 |
A | GLU174 |
A | ASN175 |
A | LYS178 |
site_id | AD9 |
Number of Residues | 5 |
Details | binding site for residue EDO A 1120 |
Chain | Residue |
A | GLU47 |
A | PHE59 |
A | GLY60 |
A | GLU353 |
A | LEU46 |
site_id | AE1 |
Number of Residues | 5 |
Details | binding site for residue EDO A 1121 |
Chain | Residue |
A | ARG61 |
A | PRO336 |
A | VAL337 |
A | LYS338 |
A | HOH1217 |
site_id | AE2 |
Number of Residues | 1 |
Details | binding site for residue FMT A 1122 |
Chain | Residue |
A | HOH1257 |
site_id | AE3 |
Number of Residues | 8 |
Details | binding site for residue EDO B 1501 |
Chain | Residue |
B | ALA208 |
B | GLN225 |
B | HIS228 |
B | ILE229 |
B | PRO230 |
B | HOH1652 |
B | HOH1670 |
B | HOH1727 |
site_id | AE4 |
Number of Residues | 2 |
Details | binding site for residue ACT B 1502 |
Chain | Residue |
B | TYR222 |
B | EDO1508 |
site_id | AE5 |
Number of Residues | 3 |
Details | binding site for residue ACT B 1503 |
Chain | Residue |
B | LYS141 |
B | ALA144 |
B | PRO145 |
site_id | AE6 |
Number of Residues | 4 |
Details | binding site for residue EDO B 1504 |
Chain | Residue |
B | ARG209 |
B | LYS212 |
B | GLU213 |
B | ACT1505 |
site_id | AE7 |
Number of Residues | 1 |
Details | binding site for residue ACT B 1505 |
Chain | Residue |
B | EDO1504 |
site_id | AE8 |
Number of Residues | 3 |
Details | binding site for residue ACT B 1506 |
Chain | Residue |
B | MET296 |
B | EDO1507 |
B | MRD1509 |
site_id | AE9 |
Number of Residues | 4 |
Details | binding site for residue EDO B 1507 |
Chain | Residue |
B | ILE271 |
B | MET296 |
B | ACT1506 |
B | HOH1736 |
site_id | AF1 |
Number of Residues | 4 |
Details | binding site for residue EDO B 1508 |
Chain | Residue |
B | ASN215 |
B | PRO217 |
B | TYR222 |
B | ACT1502 |
site_id | AF2 |
Number of Residues | 6 |
Details | binding site for residue MRD B 1509 |
Chain | Residue |
A | TYR250 |
B | ARG38 |
B | GLY39 |
B | VAL40 |
B | ACT1506 |
B | HOH1712 |
site_id | AF3 |
Number of Residues | 29 |
Details | binding site for residue NAD B 1510 |
Chain | Residue |
A | GLY284 |
A | VAL285 |
A | HIS288 |
A | ASP313 |
A | SER315 |
A | ASP316 |
A | SER317 |
A | EDO1118 |
B | THR104 |
B | SER105 |
B | ASN106 |
B | LEU107 |
B | SER109 |
B | THR131 |
B | ALA132 |
B | GLY133 |
B | GLU136 |
B | GLU137 |
B | ASP238 |
B | GLY282 |
B | GLY283 |
B | ASN307 |
B | THR308 |
B | ALA309 |
B | ALA341 |
B | ASP342 |
B | ALA343 |
B | HOH1602 |
B | HOH1650 |
site_id | AF4 |
Number of Residues | 4 |
Details | binding site for residue BME B 1511 |
Chain | Residue |
B | ARG32 |
B | ALA48 |
B | THR51 |
B | HOH1627 |
site_id | AF5 |
Number of Residues | 3 |
Details | binding site for residue ACT B 1512 |
Chain | Residue |
B | CYS142 |
B | ILE214 |
B | ASN216 |
site_id | AF6 |
Number of Residues | 3 |
Details | binding site for residue ACT B 1513 |
Chain | Residue |
B | PRO185 |
B | GLU213 |
B | HOH1692 |
site_id | AF7 |
Number of Residues | 1 |
Details | binding site for residue ACT B 1514 |
Chain | Residue |
B | TYR250 |
site_id | AF8 |
Number of Residues | 4 |
Details | binding site for residue EDO B 1516 |
Chain | Residue |
B | GLN64 |
B | ASN67 |
B | ALA68 |
B | GLU71 |
site_id | AF9 |
Number of Residues | 3 |
Details | binding site for residue EDO B 1517 |
Chain | Residue |
B | GLN30 |
B | ARG32 |
B | HOH1681 |
site_id | AG1 |
Number of Residues | 8 |
Details | binding site for residue EDO B 1518 |
Chain | Residue |
A | GLY239 |
A | SER240 |
A | NAD1105 |
B | HIS288 |
B | TRP327 |
B | LYS329 |
B | HOH1612 |
B | HOH1618 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 2 |
Details | ACT_SITE: Nucleophile => ECO:0000269|PubMed:9405486 |
Chain | Residue | Details |
A | LYS329 | |
B | LYS329 |
site_id | SWS_FT_FI2 |
Number of Residues | 14 |
Details | BINDING: BINDING => ECO:0000269|PubMed:9493264 |
Chain | Residue | Details |
A | SER105 | |
B | GLU137 | |
B | ASP238 | |
B | GLY283 | |
B | THR308 | |
B | ASP342 | |
A | THR131 | |
A | GLU137 | |
A | ASP238 | |
A | GLY283 | |
A | THR308 | |
A | ASP342 | |
B | SER105 | |
B | THR131 |
site_id | SWS_FT_FI3 |
Number of Residues | 10 |
Details | BINDING: BINDING => ECO:0000305 |
Chain | Residue | Details |
A | GLU136 | |
B | GLU323 | |
A | ASP243 | |
A | HIS288 | |
A | GLY314 | |
A | GLU323 | |
B | GLU136 | |
B | ASP243 | |
B | HIS288 | |
B | GLY314 |
site_id | SWS_FT_FI4 |
Number of Residues | 2 |
Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17525332, ECO:0007744|PubMed:20068231 |
Chain | Residue | Details |
A | SER78 | |
B | SER78 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 3 |
Details | M-CSA 687 |
Chain | Residue | Details |
A | GLU137 | electrostatic stabiliser |
A | HIS288 | proton acceptor, proton donor |
A | LYS329 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor |
site_id | MCSA2 |
Number of Residues | 3 |
Details | M-CSA 687 |
Chain | Residue | Details |
B | GLU137 | electrostatic stabiliser |
B | HIS288 | proton acceptor, proton donor |
B | LYS329 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor |