6U4P: Alpha-hemolysin

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus. Determined by X-ray diffraction at 2.49 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 2.49 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 16,814
Mol. weight: 241.06 kDa
Ligands: PQJ
Released: 25 Mar 2020

Explore 6U4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U4P 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.

Chain A: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	1
β-strand	14	1	2
β-strand	20-29	10	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	109-127	19	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

Chain B: 6 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	20-29	10	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
α-helix	105-108	4
β-strand	111-127	17	6
β-strand	132-151	20	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

Chains C, D and G: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	14
β-strand	14	1	9
β-strand	20-29	10	10
β-strand	34-43	10	10
β-strand	48	1	15
β-strand	51-61	11	10
β-strand	66-70	5	16
β-strand	75-89	15	16
β-strand	97-102	6	10
α-helix	105-108	4
β-strand	111-127	17	6
β-strand	132-149	18	6
β-strand	153-158	6	16
β-strand	164-171	8	16
β-strand	174-176	3	17
β-strand	179-182	4	17
β-strand	188	1	16
β-strand	192	1	16
β-strand	197	1	18
α-helix	206-208	3
β-strand	210	1	18
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-220	3
β-strand	224	1	10
β-strand	228-234	7	10
β-strand	242-260	19	16
β-strand	265-285	21	16
β-strand	290-292	3	16

Chains E and F: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	24
β-strand	14	1	19
β-strand	20-29	10	20
β-strand	34-43	10	20
β-strand	48	1	25
β-strand	51-61	11	20
β-strand	66-70	5	26
β-strand	75-89	15	26
β-strand	97-102	6	20
α-helix	105-108	4
β-strand	111-127	17	6
β-strand	132-149	18	6
β-strand	153-158	6	26
β-strand	164-171	8	26
β-strand	174-176	3	27
β-strand	179-182	4	27
β-strand	188	1	26
β-strand	192	1	26
β-strand	197	1	28
α-helix	206-208	3
β-strand	210	1	28
α-helix	213-215	3
α-helix	218-220	3
β-strand	224	1	20
β-strand	228-234	7	20
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, F, G	protein	293	Staphylococcus aureus	P09616 (AlphaFold model)

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

>6U4P_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMAKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Ligands and cofactors

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

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
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
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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