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 | 0042802 | molecular_function | identical protein binding |
| A | 0046203 | biological_process | spermidine catabolic process |
| A | 0051604 | biological_process | protein maturation |
| 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 | 0042802 | molecular_function | identical protein binding |
| B | 0046203 | biological_process | spermidine catabolic process |
| B | 0051604 | biological_process | protein maturation |
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 | Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"9405486","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 22 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"9493264","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 22 |
| Details | Binding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17525332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
Catalytic Information from CSA
| site_id | MCSA1 |
| Number of Residues | 3 |
| Details | M-CSA 687 |
| Chain | Residue | Details |
| A | GLU137 | electrostatic stabiliser |
| A | ASN292 | proton acceptor, proton donor |
| A | ASP333 | 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 | ASN292 | proton acceptor, proton donor |
| B | ASP333 | covalently attached, electron pair acceptor, electron pair donor, nucleofuge, nucleophile, proton acceptor, proton donor |
