1S3R: Human-specific toxin intermedilysin

Crystal structure of the human-specific toxin intermedilysin. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Jan 2005.

Method
X-ray diffraction
Resolution
2.6 Å
Organism
Streptococcus intermedius
Chains
2
Atoms
7,827
Mol. weight
118.51 kDa
Released
25 Jan 2005

Explore 1S3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S3R contains 43 α-helices and 62 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.

Chain A: 22 helices, 30 β-strands

ElementResiduesLengthSheet
α-helix57-6913
β-strand80-8231
β-strand85-8622
β-strand90-9781
β-strand100-115161
β-strand118-11923
α-helix1201
α-helix125-1273
β-strand133-13533
α-helix138-1414
α-helix145-1462
β-strand14713
α-helix1481
β-strand15214
β-strand155-15953
β-strand170-17343
α-helix178-19215
α-helix193-1975
β-strand20315
α-helix2041
β-strand205-21283
α-helix216-2238
α-helix227-2304
α-helix232-2343
α-helix238-2425
β-strand247-262163
α-helix263-2653
α-helix268-2714
β-strand27214
α-helix278-2836
β-strand292-310193
α-helix317-3259
α-helix337-3404
β-strand345-35063
β-strand360-36343
α-helix365-37410
β-strand37715
α-helix383-3842
β-strand385-39393
α-helix3981
β-strand39913
α-helix4001
β-strand402-417161
β-strand419-42576
β-strand431-442127
β-strand448-45477
β-strand46217
β-strand467-47266
β-strand476-486117
β-strand494-503107
β-strand508-51586
β-strand520-52676
Chain B: 21 helices, 32 β-strands
ElementResiduesLengthSheet
α-helix57-6913
α-helix75-784
β-strand80-8238
β-strand8617
β-strand90-9128
β-strand94-9748
β-strand100-115168
β-strand118-11929
α-helix1201
β-strand133-13539
α-helix138-1414
α-helix145-1462
β-strand14719
α-helix1481
β-strand152110
β-strand155-15959
β-strand170-17349
α-helix178-19619
β-strand203111
β-strand205-21289
α-helix216-2238
α-helix227-2304
α-helix232-2343
α-helix238-2425
β-strand247-262169
α-helix2631
α-helix268-2714
β-strand272110
α-helix2731
α-helix278-2836
β-strand292-310199
α-helix317-3237
α-helix324-3285
α-helix336-3416
β-strand343-35089
β-strand361-36339
α-helix365-37410
β-strand377111
β-strand385-39399
α-helix3981
β-strand39919
α-helix4001
β-strand402-417168
β-strand419-425712
β-strand431113
β-strand432-442112
β-strand448-45472
β-strand462113
β-strand467-472612
β-strand476-486112
β-strand494-50072
β-strand508-515812
β-strand520-526712

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
intermedilysinA, Bprotein535Streptococcus intermediusQ9LCB8 (AlphaFold model)
Sequence of entity 1 (A, B), FASTA
>1S3R_1 intermedilysin (chains A, B)
MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSETPTKPKAAQTEKKTEKKPENSNS
EAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSK
LSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPS
NSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVD
FSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSN
VSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEA
SKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYK
DGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVR
NIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVKDNTD

Primary citation

Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin. Polekhina, G., Giddings, K.S., Tweten, R.K. et al. Proc Natl Acad Sci U S A (2005) 102:600-605. DOI 10.1073/pnas.0403229101 · PubMed

Other PDB entries of the same protein (UniProt Q9LCB8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

About this viewer

MolViewer shows 1S3R directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.