Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228. Determined by X-ray diffraction at 1.89 Å resolution. Released 2 May 2012.
Explore 4DKQ in 3D Show helices and sheets RCSB PDB PDBe
4DKQ contains 13 α-helices and 28 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 |
|---|---|---|---|
| β-strand | 45-47 | 3 | 1 |
| β-strand | 53-56 | 4 | 2 |
| α-helix | 65-73 | 9 | |
| β-strand | 75-76 | 2 | 2 |
| α-helix | 77-78 | 2 | |
| β-strand | 83-85 | 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 |
| β-strand | 251 | 1 | 5 |
| β-strand | 256 | 1 | 6 |
| β-strand | 259-261 | 3 | 6 |
| α-helix | 264-266 | 3 | |
| β-strand | 271-273 | 3 | 6 |
| α-helix | 283 | 1 | |
| β-strand | 284-298 | 15 | 6 |
| β-strand | 328-334 | 7 | 6 |
| α-helix | 335-352 | 18 | |
| α-helix | 357 | 1 | |
| β-strand | 358-361 | 4 | 6 |
| α-helix | 369-372 | 4 | |
| β-strand | 374-378 | 5 | 6 |
| β-strand | 381-385 | 5 | 6 |
| α-helix | 388-391 | 4 | |
| α-helix | 393-395 | 3 | |
| 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 |
| α-helix | 457 | 1 | |
| β-strand | 465-470 | 6 | 6 |
| α-helix | 476-483 | 8 | |
| β-strand | 486-491 | 6 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| clade A/E 93TH057 HIV-1 gp120 core | A | protein | 353 | HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 | Q0ED31 |
>4DKQ_1 clade A/E 93TH057 HIV-1 gp120 core (chains A) VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM HSFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 11 |
| 0LK | N-[(1S,2S)-2-carbamimidamido-2,3-dihydro-1H-inden-1-yl]-N'-(4-chloro-3-fluoroph… | C18 H17 Cl F N5 O2 | 1 |
Water and common crystallization additives (EPE) are not listed.
Structure-Based Design, Synthesis, and Characterization of Dual Hotspot Small-Molecule HIV-1 Entry Inhibitors. Lalonde, J.M., Kwon, Y.D., Jones, D.M. et al. J Med Chem (2012) 55:4382-4396. DOI 10.1021/jm300265j · PubMed
Other PDB entries of the same protein (UniProt Q0ED31), best resolution first:
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