4YHD: Alpha-hemolysin

Staphylococcal alpha-hemolysin H35A mutant monomer. Determined by X-ray diffraction at 2.8 Å resolution. Released 21 Oct 2015.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Staphylococcus aureus
Chains: 6
Atoms: 13,502
Mol. weight: 206.81 kDa
Released: 21 Oct 2015

Explore 4YHD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4YHD contains 25 α-helices and 142 β-strands across 6 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: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
β-strand	18-29	12	1
β-strand	34-45	12	1
β-strand	50-62	13	1
β-strand	66-71	6	2
β-strand	75-89	15	2
β-strand	97-102	6	1
β-strand	107	1	2
β-strand	111-118	8	3
β-strand	124-127	4	3
β-strand	140-149	10	3
β-strand	153-157	5	2
β-strand	164-171	8	2
β-strand	174	1	4
β-strand	182	1	4
β-strand	192	1	2
β-strand	197	1	5
α-helix	206-208	3
β-strand	210	1	5
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	223-224	2	1
β-strand	228-235	8	1
β-strand	242-260	19	2
β-strand	265-285	21	2
β-strand	290-293	4	2

Chain B: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	6
β-strand	18-29	12	6
β-strand	34-45	12	6
β-strand	50-62	13	6
β-strand	66-71	6	7
β-strand	75-89	15	7
β-strand	97-102	6	6
β-strand	107	1	7
β-strand	111-118	8	8
β-strand	124-125	2	8
β-strand	140-149	10	8
β-strand	153-157	5	7
β-strand	164-171	8	7
β-strand	174-176	3	9
β-strand	179-182	4	9
β-strand	192	1	7
β-strand	197	1	10
α-helix	206-208	3
β-strand	210	1	10
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	223-224	2	6
β-strand	228-235	8	6
β-strand	242-260	19	7
β-strand	265-285	21	7
β-strand	290-293	4	7

Chain C: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	11
β-strand	18-29	12	11
β-strand	34-45	12	11
β-strand	50-62	13	11
β-strand	66-70	5	12
β-strand	75-89	15	12
β-strand	97-102	6	11
β-strand	107	1	12
β-strand	111-118	8	13
β-strand	124-126	3	13
β-strand	140-149	10	13
β-strand	153-157	5	12
β-strand	164-171	8	12
β-strand	174	1	14
β-strand	182	1	14
β-strand	188	1	12
β-strand	192	1	12
β-strand	197	1	15
α-helix	206-208	3
β-strand	210	1	15
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	223-224	2	11
β-strand	228-235	8	11
β-strand	242-260	19	12
β-strand	265-285	21	12
β-strand	290-293	4	12

Chain D: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	16
β-strand	18-29	12	16
β-strand	34-45	12	16
β-strand	50-62	13	16
β-strand	66-70	5	17
α-helix	72-74	3
β-strand	75-89	15	17
β-strand	97-102	6	16
β-strand	107	1	17
β-strand	111-119	9	18
β-strand	123-127	5	18
β-strand	140-149	10	18
β-strand	153-158	6	17
β-strand	164-171	8	17
β-strand	174-176	3	19
β-strand	179-182	4	19
β-strand	192	1	17
β-strand	197	1	20
α-helix	206-208	3
β-strand	210	1	20
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	223-224	2	16
β-strand	228-235	8	16
β-strand	242-260	19	17
β-strand	265-285	21	17
β-strand	290-293	4	17

Chain E: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	21
β-strand	19-29	11	21
β-strand	34-44	11	21
β-strand	52-62	11	21
β-strand	66-71	6	22
β-strand	75-89	15	22
β-strand	97-102	6	21
β-strand	107	1	22
β-strand	111-117	7	23
β-strand	126-127	2	23
β-strand	141-149	9	23
β-strand	153-158	6	22
β-strand	164-171	8	22
β-strand	174-176	3	24
β-strand	179-182	4	24
β-strand	188	1	22
β-strand	192	1	22
β-strand	197	1	25
α-helix	206-208	3
β-strand	210	1	25
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	223-224	2	21
β-strand	227-233	7	21
β-strand	242-260	19	22
β-strand	265-285	21	22
β-strand	290-292	3	22

Chain G: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	21
β-strand	18-29	12	21
β-strand	34-45	12	21
β-strand	50-62	13	21
β-strand	66-70	5	26
β-strand	71	1	27
β-strand	73	1	27
β-strand	75-89	15	26
β-strand	97-102	6	21
β-strand	107	1	26
β-strand	111-119	9	28
β-strand	123-125	3	28
β-strand	139-149	11	28
β-strand	153-158	6	26
β-strand	164-171	8	26
β-strand	174	1	29
β-strand	182	1	29
β-strand	192	1	26
β-strand	197	1	30
α-helix	206-208	3
β-strand	210	1	30
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	223-224	2	21
β-strand	228-235	8	21
β-strand	242-260	19	26
β-strand	265-285	21	26
β-strand	290-292	3	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-hemolysin	A, B, C, D, E, G	protein	302	Staphylococcus aureus	P09616 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, G), FASTA

>4YHD_1 Alpha-hemolysin (chains A, B, C, D, E, G)
MADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMAKKVFYSFIDDKNHNKKLLVIRTKG
TIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYG
FNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNW
GPYDRDSWNPVYGNQLFMKTRNGSMKAAENFLDPNKASSLLSSGFSPDFATVITMDRKAS
KQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTNLEHHHH
HH

Primary citation

Structural basis for pore-forming mechanism of staphylococcal alpha-hemolysin. Sugawara, T., Yamashita, D., Kato, K. et al. Toxicon (2015) 108:226-231. DOI 10.1016/j.toxicon.2015.09.033 · PubMed

Other PDB entries of the same protein (UniProt P09616 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AHL 1.89 Å, Alpha-hemolysin from staphylococcus aureus
3M4D 1.9 Å, Crystal structure of the M113N mutant of alpha-hemolysin
3M2L 2.1 Å, Crystal structure of the M113F mutant of alpha-hemolysin
3M3R 2.2 Å, Crystal structure of the M113F alpha-hemolysin mutant complexed with beta-cyclodextrin
8JX2 2.2 Å, alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer
8JX3 2.2 Å, alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head 14-mer
3M4E 2.3 Å, Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin
6U49 2.35 Å, Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant…
9SVZ 2.4 Å, The structure of S. aureus alpha-hemolysin in complex with a bicyclic peptide inhibitor
6U4P 2.49 Å, Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant…
6U3T 2.79 Å, Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant…
9M4P 3.1 Å, Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC

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