Toxin receptor complex. Determined by X-ray diffraction at 2.7 Å resolution. Released 24 Aug 2016.
Explore 5IMT in 3D Show helices and sheets RCSB PDB PDBe
5IMT contains 18 α-helices and 34 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 |
|---|---|---|---|
| α-helix | 59-69 | 11 | |
| β-strand | 80-82 | 3 | 1 |
| β-strand | 91-97 | 7 | 1 |
| β-strand | 100-115 | 16 | 1 |
| β-strand | 118-119 | 2 | 2 |
| β-strand | 133-135 | 3 | 2 |
| α-helix | 138-141 | 4 | |
| β-strand | 147 | 1 | 2 |
| β-strand | 152 | 1 | 3 |
| β-strand | 155-159 | 5 | 2 |
| β-strand | 170-173 | 4 | 2 |
| α-helix | 178-195 | 18 | |
| β-strand | 203 | 1 | 4 |
| β-strand | 205-212 | 8 | 2 |
| α-helix | 216-223 | 8 | |
| α-helix | 227-230 | 4 | |
| α-helix | 232-234 | 3 | |
| α-helix | 239-243 | 5 | |
| β-strand | 247-261 | 15 | 2 |
| α-helix | 263-265 | 3 | |
| α-helix | 268-271 | 4 | |
| β-strand | 272 | 1 | 3 |
| α-helix | 278-283 | 6 | |
| β-strand | 292-310 | 19 | 2 |
| α-helix | 317-324 | 8 | |
| β-strand | 344-351 | 8 | 2 |
| β-strand | 359-361 | 3 | 2 |
| α-helix | 367-374 | 8 | |
| β-strand | 377 | 1 | 4 |
| α-helix | 383-384 | 2 | |
| β-strand | 385-393 | 9 | 2 |
| α-helix | 398 | 1 | |
| β-strand | 399 | 1 | 2 |
| α-helix | 400 | 1 | |
| β-strand | 402-417 | 16 | 1 |
| β-strand | 419-425 | 7 | 5 |
| β-strand | 431-442 | 12 | 6 |
| β-strand | 448-454 | 7 | 6 |
| β-strand | 461-462 | 2 | 6 |
| β-strand | 466-472 | 7 | 5 |
| β-strand | 476-486 | 11 | 6 |
| β-strand | 494-503 | 10 | 6 |
| β-strand | 508-515 | 8 | 5 |
| β-strand | 520-526 | 7 | 5 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-4 | 3 | 7 |
| β-strand | 16-18 | 3 | 7 |
| β-strand | 25-31 | 7 | 6 |
| β-strand | 34-40 | 7 | 6 |
| α-helix | 42-44 | 3 | |
| α-helix | 47-53 | 7 | |
| β-strand | 60-64 | 5 | 6 |
| α-helix | 72-74 | 3 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Intermedilysin | A | protein | 534 | Streptococcus intermedius | Q9LCB8 (AlphaFold model) |
| CD59 glycoprotein | D | protein | 77 | Homo sapiens | P13987 (AlphaFold model) |
>5IMT_1 Intermedilysin (chains A) GGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSETPTKPKAAQTEKKPEKKPENSNSE AAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSKL SVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPSN STVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVDF SSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNV SYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKICAVVLGGNPGEAS KVCTGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYKD GALTLNHDGAFVARFYVYWEELGHDAEGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVRN IRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVKDNTD
>5IMT_2 CD59 glycoprotein (chains D) LQCYNCPNPTADCKTAVNCSSAFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENELT YYCCKKDLCNFNEQLEN
Water and common crystallization additives (PGE, SO4) are not listed.
Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins. Lawrence, S.L., Gorman, M.A., Feil, S.C. et al. Structure (2016) 24:1488-1498. DOI 10.1016/j.str.2016.06.017 · PubMed
Other PDB entries of the same protein (UniProt Q9LCB8 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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