6XXK
Crystal Structure of Human Deoxyhypusine Synthase in complex with spermidine
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 | 12 |
| Details | binding site for residue SPD A 401 |
| Chain | Residue |
| A | HIS288 |
| B | SER240 |
| B | ASP243 |
| B | HOH656 |
| A | ASN292 |
| A | LEU295 |
| A | ASP316 |
| A | GLU323 |
| A | TRP327 |
| A | LYS329 |
| A | HOH649 |
| A | HOH664 |
| site_id | AC2 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 402 |
| Chain | Residue |
| A | ASN106 |
| A | GLY282 |
| A | ASP342 |
| A | ALA343 |
| A | EDO408 |
| A | HOH544 |
| B | ASP313 |
| site_id | AC3 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 403 |
| Chain | Residue |
| A | PRO185 |
| A | ILE186 |
| A | GLN189 |
| A | GLU213 |
| A | FMT422 |
| site_id | AC4 |
| Number of Residues | 7 |
| Details | binding site for residue EDO A 404 |
| Chain | Residue |
| A | SER90 |
| A | HIS228 |
| A | ILE229 |
| A | PRO230 |
| A | HOH530 |
| A | HOH564 |
| A | HOH655 |
| site_id | AC5 |
| Number of Residues | 4 |
| Details | binding site for residue EDO A 405 |
| Chain | Residue |
| A | ALA68 |
| A | LYS72 |
| A | TYR302 |
| A | HOH508 |
| site_id | AC6 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 406 |
| Chain | Residue |
| A | ARG92 |
| A | PRO93 |
| A | THR95 |
| A | ASN123 |
| A | HOH502 |
| site_id | AC7 |
| Number of Residues | 5 |
| Details | binding site for residue EDO A 407 |
| Chain | Residue |
| A | ASN67 |
| A | GLU71 |
| A | LYS358 |
| A | HOH508 |
| A | HOH572 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue EDO A 408 |
| Chain | Residue |
| A | GLY282 |
| A | GLY283 |
| A | ASN307 |
| A | THR308 |
| A | EDO402 |
| B | ASP313 |
| site_id | AC9 |
| Number of Residues | 1 |
| Details | binding site for residue EDO A 409 |
| Chain | Residue |
| A | LYS205 |
| site_id | AD1 |
| Number of Residues | 3 |
| Details | binding site for residue ACT A 410 |
| Chain | Residue |
| A | GLU180 |
| A | PHE247 |
| A | ACT412 |
| site_id | AD2 |
| Number of Residues | 2 |
| Details | binding site for residue ACT A 411 |
| Chain | Residue |
| A | GLY50 |
| B | LEU148 |
| site_id | AD3 |
| Number of Residues | 4 |
| Details | binding site for residue ACT A 412 |
| Chain | Residue |
| A | CSS177 |
| A | GLU180 |
| A | ASP181 |
| A | ACT410 |
| site_id | AD4 |
| Number of Residues | 6 |
| Details | binding site for residue BME A 414 |
| Chain | Residue |
| A | TYR176 |
| A | HOH538 |
| B | LEU295 |
| B | TRP327 |
| B | SPD401 |
| B | HOH557 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue BME A 415 |
| Chain | Residue |
| A | LEU87 |
| A | THR88 |
| A | GLN89 |
| A | GLU261 |
| A | ARG264 |
| A | LEU265 |
| A | THR268 |
| site_id | AD6 |
| Number of Residues | 5 |
| Details | binding site for residue BME A 416 |
| Chain | Residue |
| A | LEU143 |
| A | ILE214 |
| A | ASN216 |
| A | FMT421 |
| A | HOH505 |
| site_id | AD7 |
| Number of Residues | 8 |
| Details | binding site for residue FMT A 417 |
| Chain | Residue |
| A | ARG32 |
| A | GLY33 |
| A | TYR34 |
| A | ARG38 |
| A | ALA48 |
| A | THR51 |
| A | HOH536 |
| A | HOH582 |
| site_id | AD8 |
| Number of Residues | 3 |
| Details | binding site for residue FMT A 418 |
| Chain | Residue |
| A | GLU311 |
| A | TYR340 |
| A | HOH534 |
| site_id | AD9 |
| Number of Residues | 6 |
| Details | binding site for residue FMT A 419 |
| Chain | Residue |
| A | ASN58 |
| A | ARG61 |
| A | VAL337 |
| A | LYS338 |
| A | TYR340 |
| A | HOH628 |
| site_id | AE1 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 420 |
| Chain | Residue |
| B | GLU174 |
| A | SER21 |
| A | SER22 |
| B | PRO172 |
| site_id | AE2 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 421 |
| Chain | Residue |
| A | ILE214 |
| A | ASN215 |
| A | BME416 |
| B | GLN79 |
| site_id | AE3 |
| Number of Residues | 4 |
| Details | binding site for residue FMT A 422 |
| Chain | Residue |
| A | TRP182 |
| A | EDO403 |
| A | HOH504 |
| A | HOH565 |
| site_id | AE4 |
| Number of Residues | 2 |
| Details | binding site for residue FMT A 423 |
| Chain | Residue |
| A | HOH539 |
| A | HOH577 |
| site_id | AE5 |
| Number of Residues | 11 |
| Details | binding site for residue SPD B 401 |
| Chain | Residue |
| A | SER240 |
| A | ASP243 |
| A | BME414 |
| A | HOH636 |
| B | HIS288 |
| B | ASN292 |
| B | LEU295 |
| B | ASP316 |
| B | GLU323 |
| B | TRP327 |
| B | LYS329 |
| site_id | AE6 |
| Number of Residues | 5 |
| Details | binding site for residue MRD B 402 |
| Chain | Residue |
| A | PHE247 |
| B | ARG38 |
| B | VAL40 |
| B | ACT410 |
| B | HOH636 |
| site_id | AE7 |
| Number of Residues | 2 |
| Details | binding site for residue EDO B 403 |
| Chain | Residue |
| B | LYS212 |
| B | GLU213 |
| site_id | AE8 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 404 |
| Chain | Residue |
| B | ARG320 |
| B | PRO321 |
| B | ASP322 |
| B | ACT412 |
| B | HOH646 |
| site_id | AE9 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 405 |
| Chain | Residue |
| A | ASP313 |
| B | ASN106 |
| B | GLY282 |
| B | ALA343 |
| B | HOH524 |
| site_id | AF1 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 406 |
| Chain | Residue |
| B | ARG32 |
| B | TYR34 |
| B | ARG38 |
| B | ALA48 |
| B | HOH590 |
| site_id | AF2 |
| Number of Residues | 5 |
| Details | binding site for residue EDO B 407 |
| Chain | Residue |
| B | GLN194 |
| B | ASN195 |
| B | PRO253 |
| B | GLY254 |
| B | HOH548 |
| site_id | AF3 |
| Number of Residues | 8 |
| Details | binding site for residue EDO B 408 |
| Chain | Residue |
| B | LYS287 |
| B | TYR305 |
| B | ASP316 |
| B | ALA319 |
| B | ARG320 |
| B | GLU323 |
| B | ALA324 |
| B | HOH522 |
| site_id | AF4 |
| Number of Residues | 3 |
| Details | binding site for residue ACT B 409 |
| Chain | Residue |
| B | CYS142 |
| B | ILE214 |
| B | ASN216 |
| site_id | AF5 |
| Number of Residues | 4 |
| Details | binding site for residue ACT B 410 |
| Chain | Residue |
| B | MET296 |
| B | MRD402 |
| B | FMT417 |
| B | HOH530 |
| site_id | AF6 |
| Number of Residues | 6 |
| Details | binding site for residue ACT B 411 |
| Chain | Residue |
| A | HOH512 |
| A | HOH650 |
| A | HOH678 |
| B | ASP316 |
| B | HOH535 |
| B | HOH653 |
| site_id | AF7 |
| Number of Residues | 6 |
| Details | binding site for residue ACT B 412 |
| Chain | Residue |
| A | SER152 |
| A | ARG154 |
| B | ARG320 |
| B | EDO404 |
| B | HOH558 |
| B | HOH570 |
| site_id | AF8 |
| Number of Residues | 3 |
| Details | binding site for residue ACT B 413 |
| Chain | Residue |
| B | LYS141 |
| B | LEU143 |
| B | ALA144 |
| site_id | AF9 |
| Number of Residues | 7 |
| Details | binding site for residue BME B 414 |
| Chain | Residue |
| A | ASN58 |
| A | ARG61 |
| B | GLU150 |
| B | PHE151 |
| B | SER152 |
| B | ASN168 |
| B | HOH691 |
| site_id | AG1 |
| Number of Residues | 4 |
| Details | binding site for residue FMT B 415 |
| Chain | Residue |
| B | HIS228 |
| B | HOH519 |
| B | HOH540 |
| B | HOH564 |
| site_id | AG2 |
| Number of Residues | 1 |
| Details | binding site for residue FMT B 416 |
| Chain | Residue |
| B | LYS178 |
| site_id | AG3 |
| Number of Residues | 3 |
| Details | binding site for residue FMT B 417 |
| Chain | Residue |
| B | LEU295 |
| B | ACT410 |
| B | HOH640 |
| site_id | AG4 |
| Number of Residues | 2 |
| Details | binding site for residue FMT B 418 |
| Chain | Residue |
| B | GLN65 |
| B | HOH505 |
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 |
