6XXJ
Crystal Structure of Human Deoxyhypusine Synthase in complex with spermidine and 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-hypusine biosynthetic process |
| 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-hypusine biosynthetic process |
| 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 | 11 |
| Details | binding site for residue SPD A 401 |
| Chain | Residue |
| A | HIS288 |
| B | ASP243 |
| B | NAD404 |
| A | ASN292 |
| A | LEU295 |
| A | ASP316 |
| A | GLU323 |
| A | TRP327 |
| A | LYS329 |
| A | FMT413 |
| A | HOH692 |
| site_id | AC2 |
| Number of Residues | 31 |
| Details | binding site for residue NAD A 402 |
| 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 | ALA341 |
| A | ASP342 |
| A | ALA343 |
| A | HOH508 |
| A | HOH601 |
| A | HOH696 |
| B | GLY284 |
| B | VAL285 |
| B | HIS288 |
| B | ASP313 |
| B | SER315 |
| B | ASP316 |
| B | SER317 |
| B | SPD401 |
| B | NAD404 |
| B | FMT413 |
| site_id | AC3 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 403 |
| Chain | Residue |
| A | GLU160 |
| A | ASN161 |
| A | HOH631 |
| site_id | AC4 |
| Number of Residues | 2 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | SER22 |
| A | THR23 |
| site_id | AC5 |
| Number of Residues | 3 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | GLN194 |
| A | HOH554 |
| A | HOH642 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | GLU150 |
| A | SER152 |
| A | LEU153 |
| A | HOH529 |
| A | HOH707 |
| site_id | AC7 |
| Number of Residues | 1 |
| Details | binding site for residue ACT A 407 |
| Chain | Residue |
| A | ALA85 |
| site_id | AC8 |
| Number of Residues | 4 |
| Details | binding site for residue BME A 408 |
| Chain | Residue |
| A | ARG61 |
| A | PRO336 |
| A | VAL337 |
| A | LYS338 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue BME A 409 |
| Chain | Residue |
| A | TYR176 |
| A | HOH567 |
| B | LEU295 |
| B | TRP327 |
| B | SPD401 |
| B | HOH591 |
| site_id | AD1 |
| Number of Residues | 5 |
| Details | binding site for residue BME A 410 |
| Chain | Residue |
| A | LEU87 |
| A | GLU261 |
| A | ARG264 |
| A | LEU265 |
| A | THR268 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue BME A 411 |
| Chain | Residue |
| A | ILE214 |
| A | ASN216 |
| A | HOH569 |
| A | HOH701 |
| site_id | AD3 |
| Number of Residues | 5 |
| Details | binding site for residue FMT A 412 |
| Chain | Residue |
| A | ASN298 |
| A | HOH503 |
| A | HOH521 |
| A | HOH627 |
| B | ARG159 |
| site_id | AD4 |
| Number of Residues | 9 |
| Details | binding site for residue FMT A 413 |
| Chain | Residue |
| A | GLY314 |
| A | SER315 |
| A | ASP316 |
| A | GLU323 |
| A | SPD401 |
| B | ASN106 |
| B | ILE166 |
| B | GLY167 |
| B | NAD404 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue FMT A 414 |
| Chain | Residue |
| A | GLY33 |
| A | ARG38 |
| A | ALA48 |
| A | THR51 |
| A | HOH504 |
| A | HOH548 |
| A | HOH662 |
| site_id | AD6 |
| Number of Residues | 12 |
| Details | binding site for residue SPD B 401 |
| Chain | Residue |
| A | BME409 |
| B | HIS288 |
| B | ASN292 |
| B | LEU295 |
| B | ASP316 |
| B | GLU323 |
| B | TRP327 |
| B | LYS329 |
| B | FMT413 |
| A | SER240 |
| A | ASP243 |
| A | NAD402 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 402 |
| Chain | Residue |
| B | GLN225 |
| B | HIS228 |
| B | ILE229 |
| B | PRO230 |
| B | EDO407 |
| B | HOH514 |
| B | HOH605 |
| B | HOH721 |
| site_id | AD8 |
| Number of Residues | 6 |
| Details | binding site for residue MRD B 403 |
| Chain | Residue |
| A | TYR250 |
| B | ARG38 |
| B | VAL40 |
| B | THR268 |
| B | EDO405 |
| B | HOH629 |
| site_id | AD9 |
| Number of Residues | 30 |
| Details | binding site for residue NAD B 404 |
| Chain | Residue |
| A | GLY284 |
| A | VAL285 |
| A | HIS288 |
| A | ASP313 |
| A | SER315 |
| A | ASP316 |
| A | SER317 |
| A | SPD401 |
| A | NAD402 |
| A | FMT413 |
| 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 | HOH617 |
| site_id | AE1 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| B | MET296 |
| B | MRD403 |
| B | HOH599 |
| site_id | AE2 |
| Number of Residues | 3 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | LYS212 |
| B | GLU213 |
| B | ASN215 |
| site_id | AE3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | PRO230 |
| B | LEU265 |
| B | GLN269 |
| B | EDO402 |
| B | HOH706 |
| site_id | AE4 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| A | ASN195 |
| A | HOH511 |
| A | HOH730 |
| B | ARG43 |
| B | GLN357 |
| site_id | AE5 |
| Number of Residues | 3 |
| Details | binding site for residue ACT B 410 |
| Chain | Residue |
| B | CYS142 |
| B | ILE214 |
| B | ASN216 |
| site_id | AE6 |
| Number of Residues | 2 |
| Details | binding site for residue ACT B 411 |
| Chain | Residue |
| B | ASN215 |
| B | PGE415 |
| site_id | AE7 |
| Number of Residues | 3 |
| Details | binding site for residue ACT B 412 |
| Chain | Residue |
| B | LYS141 |
| B | LEU143 |
| B | ALA144 |
| site_id | AE8 |
| Number of Residues | 8 |
| Details | binding site for residue FMT B 413 |
| Chain | Residue |
| A | ILE166 |
| A | GLY167 |
| A | NAD402 |
| B | GLY314 |
| B | SER315 |
| B | ASP316 |
| B | GLU323 |
| B | SPD401 |
| site_id | AE9 |
| Number of Residues | 1 |
| Details | binding site for residue FMT B 414 |
| Chain | Residue |
| B | ALA361 |
| site_id | AF1 |
| Number of Residues | 9 |
| Details | binding site for residue PGE B 415 |
| Chain | Residue |
| B | ARG117 |
| B | GLN121 |
| B | PRO217 |
| B | TYR222 |
| B | TRP223 |
| B | LYS226 |
| B | ACT411 |
| B | HOH507 |
| B | HOH741 |
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 | 2 |
| 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 |
