Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 2.3 angstrom, native-SAD phasing). Determined by X-ray diffraction at 2.3 Å resolution. Released 7 Jun 2017.
Explore 5GNB in 3D Show helices and sheets RCSB PDB PDBe
5GNB contains 21 α-helices and 34 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 312-315 | 4 | |
| β-strand | 317-319 | 3 | 1 |
| α-helix | 320-321 | 2 | |
| α-helix | 324-325 | 2 | |
| β-strand | 326 | 1 | 2 |
| α-helix | 329-333 | 5 | |
| β-strand | 337-339 | 3 | 3 |
| α-helix | 341-343 | 3 | |
| β-strand | 345-349 | 5 | 4 |
| β-strand | 352-354 | 3 | 2 |
| α-helix | 356-362 | 7 | |
| β-strand | 364-371 | 8 | 4 |
| α-helix | 375-377 | 3 | |
| β-strand | 382-383 | 2 | 2 |
| β-strand | 385-392 | 8 | 4 |
| α-helix | 395-401 | 7 | |
| α-helix | 408-412 | 5 | |
| α-helix | 415-417 | 3 | |
| β-strand | 422-430 | 9 | 4 |
| α-helix | 431-433 | 3 | |
| β-strand | 435-437 | 3 | 3 |
| α-helix | 443-447 | 5 | |
| β-strand | 459-463 | 5 | 5 |
| β-strand | 467-468 | 2 | 6 |
| β-strand | 477 | 1 | 7 |
| α-helix | 478 | 1 | |
| α-helix | 479-482 | 4 | |
| β-strand | 487 | 1 | 8 |
| α-helix | 489-491 | 3 | |
| β-strand | 492 | 1 | 7 |
| β-strand | 494 | 1 | 9 |
| α-helix | 495-496 | 2 | |
| β-strand | 504-509 | 6 | 8 |
| β-strand | 512-518 | 7 | 8 |
| α-helix | 530-532 | 3 | |
| β-strand | 536-537 | 2 | 6 |
| α-helix | 539-541 | 3 | |
| β-strand | 551 | 1 | 10 |
| α-helix | 553-555 | 3 | |
| β-strand | 556 | 1 | 11 |
| β-strand | 558 | 1 | 7 |
| β-strand | 566 | 1 | 9 |
| β-strand | 569 | 1 | 11 |
| α-helix | 571-573 | 3 | |
| β-strand | 574 | 1 | 10 |
| β-strand | 577-581 | 5 | 5 |
| β-strand | 583-584 | 2 | 4 |
| β-strand | 587-597 | 11 | 4 |
| β-strand | 604-606 | 3 | 2 |
| β-strand | 621-626 | 6 | 1 |
| β-strand | 629-638 | 10 | 1 |
| α-helix | 640-642 | 3 | |
| β-strand | 649-651 | 3 | 1 |
| β-strand | 657-661 | 5 | 1 |
| β-strand | 668-672 | 5 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Spike glycoprotein | A | protein | 371 | Human coronavirus HKU1 (isolate N1) | Q5MQD0 (AlphaFold model) |
>5GNB_1 Spike glycoprotein (chains A) SGFTVKPVATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTD SFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLY YSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCK SHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHC AGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCS NDLLQPNTEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDSNGNIIGFKDFVTN KTYNIFPCYAG
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 4 |
Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1. Ou, X., Guan, H., Qin, B. et al. Nat Commun (2017) 8:15216-15216. DOI 10.1038/ncomms15216 · PubMed
Other PDB entries of the same protein (UniProt Q5MQD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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