6U3T: Alpha-hemolysin

Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus. Determined by X-ray diffraction at 2.79 Å resolution. Released 25 Mar 2020.

Method: X-ray diffraction
Resolution: 2.79 Å
Organism: Staphylococcus aureus
Chains: 2
Atoms: 4,240
Mol. weight: 68.54 kDa
Ligands: PQJ
Released: 25 Mar 2020

Explore 6U3T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U3T contains 7 α-helices and 45 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: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	19-29	11	1
β-strand	34-44	11	1
β-strand	48	1	2
β-strand	50-57	8	1
β-strand	60-61	2	1
β-strand	66-71	6	3
β-strand	75-89	15	3
β-strand	97-102	6	1
β-strand	107	1	3
β-strand	111-116	6	4
β-strand	144-149	6	4
β-strand	153-158	6	3
β-strand	164-171	8	3
β-strand	174	1	5
β-strand	182	1	5
β-strand	192	1	3
β-strand	197	1	6
α-helix	206-209	4
β-strand	210	1	6
α-helix	211-212	2
α-helix	213-215	3
β-strand	224	1	1
β-strand	228-235	8	1
β-strand	242-260	19	3
β-strand	265-285	21	3
β-strand	290-292	3	3

Chain B: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	18-29	12	2
β-strand	34-45	12	2
β-strand	50-57	8	2
β-strand	60-61	2	2
β-strand	66-71	6	7
β-strand	75-89	15	7
β-strand	97-102	6	2
β-strand	107	1	7
β-strand	111-116	6	8
β-strand	144-149	6	8
β-strand	153-158	6	7
β-strand	164-171	8	7
β-strand	174	1	9
β-strand	182	1	9
β-strand	192	1	7
β-strand	197	1	10
α-helix	206-209	4
β-strand	210	1	10
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	2
β-strand	228-235	8	2
β-strand	242-260	19	7
β-strand	265-285	21	7
β-strand	290-292	3	7

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>6U3T_1 Alpha-hemolysin (chains A, B)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMAKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Ligands and cofactors

ID	Name	Formula	Copies
PQJ	fos-choline-14	C19 H43 N O4 P	4

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
6U4P 2.49 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

Browse structure collections

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