5IMW: Trapped Toxin

Name: PDB 5IMW: Trapped Toxin
Published: 2016-08-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Trapped Toxin. Determined by X-ray diffraction at 2.89 Å resolution. Released 24 Aug 2016.

Method: X-ray diffraction
Resolution: 2.89 Å
Organism: Streptococcus intermedius
Chains: 2
Atoms: 7,113
Mol. weight: 103.77 kDa
Released: 24 Aug 2016

Explore 5IMW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IMW contains 34 α-helices and 67 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: 17 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	58-70	13
α-helix	75-78	4
β-strand	80-82	3	1
β-strand	85-86	2	2
β-strand	91	1	1
β-strand	94	1	1
β-strand	97	1	1
β-strand	100-115	16	1
β-strand	118-119	2	3
β-strand	133-135	3	3
α-helix	138-141	4
β-strand	147	1	3
β-strand	155-159	5	3
α-helix	166-169	4
β-strand	170-173	4	3
α-helix	178-196	19
β-strand	203	1	4
α-helix	204	1
β-strand	205-212	8	3
α-helix	216-223	8
α-helix	227-230	4
α-helix	232-234	3
α-helix	239-243	5
β-strand	247-262	16	3
α-helix	263-265	3
α-helix	268-271	4
α-helix	278-283	6
β-strand	292-310	19	3
α-helix	317-324	8
β-strand	344-350	7	3
β-strand	360-361	2	3
α-helix	366-374	9
β-strand	377	1	4
α-helix	383-384	2
β-strand	385-393	9	3
β-strand	399	1	3
α-helix	400-401	2
β-strand	402-417	16	1
β-strand	421-425	5	5
β-strand	431-442	12	6
β-strand	448-454	7	6
β-strand	461-462	2	6
β-strand	466-470	5	5
β-strand	476-485	10	6
β-strand	495-500	6	6
β-strand	509-515	7	5
β-strand	520-526	7	5

Chain B: 17 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	58-69	12
β-strand	80-82	3	7
β-strand	85-86	2	6
β-strand	91	1	8
β-strand	94-97	4	9
β-strand	100-105	6	9
β-strand	106	1	8
β-strand	108-115	8	7
β-strand	118-119	2	10
α-helix	125-127	3
β-strand	133-135	3	10
α-helix	138-141	4
β-strand	147	1	10
β-strand	155	1	11
β-strand	157-159	3	10
β-strand	170	1	10
β-strand	173	1	11
α-helix	178-196	19
β-strand	203	1	12
α-helix	204	1
β-strand	205-212	8	10
α-helix	216-223	8
α-helix	227-231	5
α-helix	232-234	3
α-helix	239-243	5
β-strand	247-262	16	10
α-helix	263-265	3
α-helix	268-271	4
α-helix	279-283	5
β-strand	287	1	13
β-strand	290	1	13
β-strand	292-310	19	10
α-helix	317-324	8
β-strand	344-350	7	10
α-helix	352-353	2
β-strand	359-361	3	10
α-helix	366-374	9
β-strand	377	1	12
α-helix	383-384	2
β-strand	385-393	9	10
β-strand	399	1	10
β-strand	402-409	8	7
β-strand	412-417	6	9
β-strand	419-425	7	14
β-strand	431	1	15
β-strand	432-442	11	2
α-helix	447	1
β-strand	448-454	7	2
β-strand	462	1	15
β-strand	466-472	7	14
β-strand	476-484	9	2
β-strand	498-500	3	2
β-strand	509-515	7	14
β-strand	520-526	7	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Intermedilysin	A, B	protein	471	Streptococcus intermedius	Q9LCB8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IMW_1 Intermedilysin (chains A, B)
SEAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATS
KLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENP
SNSTVRTAVNNLVEKWIQKYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNV
DFSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVS
NVSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKICAVVLGGNPGE
ASKVCTGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSY
KDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNV
RNIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVV

Primary citation

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:

1S3R 2.6 Å, Crystal structure of the human-specific toxin intermedilysin
5IMT 2.7 Å, Toxin receptor complex
4BIK 3.49 Å, Structure of a disulfide locked mutant of Intermedilysin with human CD59
6ZD0 4.6 Å, Disulfide-locked early prepore intermedilysin-CD59

Browse structure collections

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