5IMY: Trapped Toxin

Trapped Toxin. Determined by X-ray diffraction at 2.4 Å resolution. Released 24 Aug 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Gardnerella vaginalis, Homo sapiens
Chains: 4
Atoms: 8,802
Mol. weight: 126.63 kDa
Released: 24 Aug 2016

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

Secondary structure: helices and β-sheets

5IMY contains 42 α-helices and 74 β-strands across 4 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, 35 β-strands

Element	Residues	Length	Sheet
α-helix	48-56	9
α-helix	64-66	3
β-strand	67-69	3	1
β-strand	77-83	7	1
β-strand	88-102	15	1
β-strand	105-106	2	2
α-helix	107	1
α-helix	112-114	3
β-strand	120-122	3	2
α-helix	125-128	4
β-strand	134	1	2
β-strand	139	1	3
α-helix	140-141	2
β-strand	142-146	5	2
β-strand	157-160	4	2
α-helix	165-179	15
α-helix	180-184	5
β-strand	190	1	4
α-helix	191	1
β-strand	192-199	8	2
α-helix	203-210	8
α-helix	214-217	4
α-helix	219-221	3
α-helix	225-229	5
β-strand	234-249	16	2
α-helix	250-251	2
β-strand	259	1	3
α-helix	266-269	4
β-strand	274	1	5
β-strand	277	1	5
β-strand	279-297	19	2
α-helix	304-312	9
α-helix	324-327	4
β-strand	331-337	7	2
α-helix	352-361	10
β-strand	364	1	4
β-strand	373-380	8	2
α-helix	385	1
β-strand	386	1	2
α-helix	387	1
β-strand	389-403	15	1
β-strand	406-415	10	6
β-strand	418	1	7
β-strand	421-429	9	8
β-strand	435-441	7	8
β-strand	449	1	7
β-strand	452-459	8	6
β-strand	464-469	6	8
β-strand	472	1	7
β-strand	477	1	9
β-strand	479	1	9
α-helix	480-481	2
β-strand	482	1	7
α-helix	483	1
β-strand	486-490	5	8
β-strand	495-503	9	6
β-strand	506-511	6	6

Chain B: 14 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	67-69	3	1
β-strand	77-81	5	1
β-strand	87	1	13
β-strand	90-102	13	1
β-strand	105-106	2	14
α-helix	109-112	4
β-strand	120-122	3	14
α-helix	125-128	4
α-helix	132-133	2
β-strand	134	1	14
β-strand	139	1	15
α-helix	140-141	2
β-strand	142-146	5	14
β-strand	157-160	4	14
α-helix	165-182	18
β-strand	192-199	8	14
α-helix	203-210	8
α-helix	214-217	4
α-helix	226-229	4
β-strand	234-249	16	14
β-strand	257	1	15
β-strand	259	1	15
α-helix	265-268	4
β-strand	279-297	19	14
α-helix	304-312	9
α-helix	322-327	6
β-strand	331-336	6	14
β-strand	344	1	14
α-helix	352-362	11
β-strand	373-380	8	14
α-helix	385	1
β-strand	386	1	14
α-helix	387	1
β-strand	389-401	13	1
β-strand	404	1	13
β-strand	406-412	7	16
β-strand	417-429	13	12
β-strand	435-441	7	12
β-strand	453-459	7	16
β-strand	464-473	10	12
β-strand	483-490	8	12
β-strand	495-502	8	16
β-strand	507-514	8	16

Chains C and D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	10
β-strand	16-18	3	10
β-strand	25-31	7	8
β-strand	34-40	7	8
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	8
α-helix	72-74	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vaginolysin	A, B	protein	490	Gardnerella vaginalis	B2YGA4 (AlphaFold model)
CD59 glycoprotein	C, D	protein	78	Homo sapiens	P13987 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5IMY_1 Vaginolysin (chains A, B)
SNAHMAPSAKDSEPATSCAAKKDSLNNYLWDLQYDKTNILARHGETIENKFSSDSFNKNG
EFVVVEHQKKNITNTTSNLSVTSANDDRVYPGALFRADKNLMDNMPSLISANRAPITLSV
DLPGFHGGESAVTVQRPTKSSVTSAVNGLVSKWNAQYGASHHVAARMQYDSASAQSMNQL
KAKFGADFAKIGVPLKIDFDAVHKGEKQTQIVNFKQTYYTVSVDAPDSPADFFAPCTTPD
SLKNRGVDNKRPPVYVSNVAYGRSMYVKFDTTSKSTDFQAAVEAAIKGVEIKPNTEFHRI
LQNTSVCAVILGGSANGAAKVCTGNIDTLKALIQEGANLSTSSPAVPIAYTTSFVKDNEV
ATLQSNSDYIETKVSSYRNGYLTLDHRGAYVARYYIYWDEYGTEIDGTPYVRSRAWEGNG
KYRTAHFNTTIQFKGNVRNLRIKLVEKTGLVWEPWRTVYDRSDLPLVRQRTISNWGTTLW
PRVAETVKND

Sequence of entity 2 (C, D), FASTA

>5IMY_2 CD59 glycoprotein (chains C, D)
MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENEL
TYYCCKKDLCNFNEQLEN

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

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