Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120. Determined by X-ray diffraction at 1.79 Å resolution. Released 19 Jun 2013.
Explore 4KA2 in 3D Show helices and sheets RCSB PDB PDBe
4KA2 contains 12 α-helices and 32 β-strands across 2 chains. 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 |
|---|---|---|---|
| β-strand | 47 | 1 | 1 |
| β-strand | 53-56 | 4 | 2 |
| α-helix | 65-73 | 9 | |
| β-strand | 74-76 | 3 | 2 |
| α-helix | 77-78 | 2 | |
| β-strand | 84-86 | 3 | 1 |
| β-strand | 91-94 | 4 | 3 |
| α-helix | 99-115 | 17 | |
| β-strand | 120-123 | 4 | 4 |
| β-strand | 199-202 | 4 | 4 |
| β-strand | 215 | 1 | 5 |
| β-strand | 216-218 | 3 | 2 |
| β-strand | 223-228 | 6 | 1 |
| β-strand | 236-239 | 4 | 3 |
| β-strand | 242-245 | 4 | 1 |
| β-strand | 247 | 1 | 2 |
| α-helix | 248-250 | 3 | |
| β-strand | 251 | 1 | 5 |
| β-strand | 256 | 1 | 6 |
| β-strand | 259-261 | 3 | 6 |
| β-strand | 271-273 | 3 | 6 |
| α-helix | 283 | 1 | |
| β-strand | 284-298 | 15 | 6 |
| β-strand | 328-334 | 7 | 6 |
| α-helix | 335-353 | 19 | |
| α-helix | 357 | 1 | |
| β-strand | 358-361 | 4 | 6 |
| β-strand | 367 | 1 | 7 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-378 | 5 | 6 |
| β-strand | 381-385 | 5 | 6 |
| α-helix | 388-391 | 4 | |
| β-strand | 393 | 1 | 6 |
| β-strand | 413-421 | 9 | 6 |
| β-strand | 423-425 | 3 | 4 |
| β-strand | 432-434 | 3 | 4 |
| α-helix | 436-439 | 4 | |
| β-strand | 443-456 | 14 | 6 |
| β-strand | 465-470 | 6 | 6 |
| α-helix | 476-483 | 8 | |
| β-strand | 486-490 | 5 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 3-11 | 9 | |
| β-strand | 17-20 | 4 | 7 |
| β-strand | 23-26 | 4 | 7 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| HIV-1 YU2 gp120 | A | protein | 376 | Human immunodeficiency virus 1 | P35961 |
| M48U12 | R | protein | 28 |
>4KA2_1 HIV-1 YU2 gp120 (chains A) MPMGSLQPLATLYLLGMLVASVLAVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDP NPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEP IPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVI RSENFTNNAKTIIVQLNESVVINCTRPNNGGSGSGGDIRQAHCNLSKTQWENTLEQIAIK LKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITL PCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMR DNWRSELYKYKVVKIE
>4KA2_2 M48U12 (chains R) XNLHFCQLRCKSLGLLGRCAPTXCACVX
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 8 |
Interfacial Cavity Filling To Optimize CD4-Mimetic Miniprotein Interactions with HIV-1 Surface Glycoprotein. Morellato-Castillo, L., Acharya, P., Combes, O. et al. J Med Chem (2013) 56:5033-5047. DOI 10.1021/jm4002988 · PubMed
Other PDB entries of the same protein (UniProt P35961), best resolution first:
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