6U49: Alpha-hemolysin

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus. Determined by X-ray diffraction at 2.35 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 2.35 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 17,541
Mol. weight: 241.5 kDa
Ligands: PQJ
Released: 25 Mar 2020

Explore 6U49 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U49 contains 39 α-helices and 168 β-strands across 7 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.

Chains A and C: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	1
β-strand	14	1	2
α-helix	19-20	2
β-strand	21-29	9	3
β-strand	34-43	10	3
β-strand	48	1	4
β-strand	51-61	11	3
β-strand	66-70	5	5
β-strand	75-89	15	5
β-strand	97-102	6	3
β-strand	111-127	17	6
β-strand	132-149	18	6
β-strand	153-158	6	5
β-strand	164-171	8	5
β-strand	174-176	3	7
β-strand	179-182	4	7
β-strand	188	1	5
β-strand	192	1	5
β-strand	197	1	8
α-helix	206-208	3
β-strand	210	1	8
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-220	3
β-strand	224	1	3
β-strand	228-234	7	3
β-strand	242-260	19	5
β-strand	265-285	21	5
β-strand	290-292	3	5

Chains B, D and E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	9
β-strand	14	1	1
β-strand	21-29	9	4
β-strand	34-43	10	4
β-strand	48	1	10
β-strand	51-61	11	4
β-strand	66-70	5	11
β-strand	75-89	15	11
β-strand	97-102	6	4
β-strand	111-127	17	6
β-strand	132-149	18	6
β-strand	153-158	6	11
β-strand	164-171	8	11
β-strand	174-176	3	12
β-strand	179-182	4	12
β-strand	188	1	11
β-strand	192	1	11
β-strand	197	1	13
α-helix	206-208	3
β-strand	210	1	13
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-220	3
β-strand	224	1	4
β-strand	228-234	7	4
β-strand	242-260	19	11
β-strand	265-285	21	11
β-strand	290-292	3	11

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	29
β-strand	14	1	24
α-helix	19-20	2
β-strand	21-29	9	25
β-strand	34-43	10	25
β-strand	48	1	30
β-strand	51-61	11	25
β-strand	66-70	5	31
β-strand	75-89	15	31
β-strand	97-102	6	25
β-strand	109-127	19	6
β-strand	132-149	18	6
β-strand	153-158	6	31
β-strand	164-171	8	31
β-strand	174-176	3	32
β-strand	179-182	4	32
β-strand	188	1	31
β-strand	192	1	31
β-strand	197	1	33
α-helix	206-208	3
β-strand	210	1	33
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-220	3
β-strand	224	1	25
β-strand	228-234	7	25
β-strand	242-260	19	31
β-strand	265-285	21	31
β-strand	290-292	3	31

Chain G: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
β-strand	14	1	29
α-helix	19-20	2
β-strand	21-29	9	30
β-strand	34-43	10	30
β-strand	48	1	3
β-strand	51-61	11	30
β-strand	66-70	5	34
β-strand	75-89	15	34
β-strand	97-102	6	30
β-strand	111-127	17	6
β-strand	132-151	20	6
β-strand	153-158	6	34
β-strand	164-171	8	34
β-strand	174-176	3	35
β-strand	179-182	4	35
β-strand	188	1	34
β-strand	192	1	34
β-strand	197	1	36
α-helix	206-208	3
β-strand	210	1	36
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	30
β-strand	228-234	7	30
β-strand	242-260	19	34
β-strand	265-285	21	34
β-strand	290-292	3	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-hemolysin	A, B, C, D, E, F, G	protein	293	Staphylococcus aureus	P09616 (AlphaFold model)

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

>6U49_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Ligands and cofactors

ID	Name	Formula	Copies
PQJ	fos-choline-14	C19 H43 N O4 P	21

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence. Liu, J., Kozhaya, L., Torres, V.J. et al. J Biol Chem (2020) 295:5944-5959. DOI 10.1074/jbc.RA120.012697 · 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
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…
4YHD 2.8 Å, Staphylococcal alpha-hemolysin H35A mutant monomer
9M4P 3.1 Å, Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC

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