9SVZ: S. aureus alpha-hemolysin

The structure of S. aureus alpha-hemolysin in complex with a bicyclic peptide inhibitor. Determined by X-ray diffraction at 2.4 Å resolution. Released 12 Aug 2026.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Staphylococcus aureus, synthetic construct
Chains: 4
Atoms: 5,155
Mol. weight: 72.21 kDa
Ligands: R06, MG
Released: 12 Aug 2026

Explore 9SVZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9SVZ contains 10 α-helices and 49 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: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	11-16	6	1
β-strand	19-30	12	1
β-strand	35-46	12	1
β-strand	51-62	12	1
β-strand	67-72	6	2
β-strand	76-90	15	2
β-strand	98-103	6	1
β-strand	108	1	2
β-strand	112-119	8	3
β-strand	125-127	3	3
β-strand	141-150	10	3
β-strand	154-158	5	2
α-helix	159-161	3
β-strand	165-172	8	2
β-strand	175-177	3	4
β-strand	180-183	4	4
β-strand	189	1	2
β-strand	193	1	2
β-strand	198	1	5
α-helix	207-209	3
β-strand	211	1	5
α-helix	212-213	2
α-helix	214-216	3
α-helix	219-221	3
β-strand	225	1	1
β-strand	229-236	8	1
β-strand	243-261	19	2
β-strand	266-286	21	2
β-strand	291-293	3	2

Chain B: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	6
β-strand	19-30	12	6
β-strand	35-46	12	6
β-strand	51-62	12	6
β-strand	67-72	6	7
β-strand	74	1	7
β-strand	76-90	15	7
β-strand	98-103	6	6
β-strand	108	1	7
β-strand	112-119	8	8
β-strand	125-128	4	8
β-strand	141-150	10	8
β-strand	154-159	6	7
β-strand	165-172	8	7
β-strand	175-176	2	9
β-strand	182-183	2	9
β-strand	189	1	7
β-strand	193	1	7
β-strand	198	1	10
α-helix	207-209	3
β-strand	211	1	10
α-helix	214-216	3
α-helix	219-222	4
β-strand	225	1	6
β-strand	229-236	8	6
β-strand	243-261	19	7
β-strand	266-286	21	7
β-strand	291-293	3	7

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-hemolysin	A, B	protein	294	Staphylococcus aureus	P09616 (AlphaFold model)
Bicyclic peptide	C, D	protein	18	synthetic construct

Sequence of entity 1 (A, B), FASTA

>9SVZ_1 Alpha-hemolysin (chains A, B)
MADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMAKKVFYSFIDDKNHNKKLLVIRTKG
TIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYG
FNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNW
GPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKAS
KQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Sequence of entity 2 (C, D), FASTA

>9SVZ_2 Bicyclic peptide (chains C, D)
ACPTLNYCWNPFMSVCAA

Ligands and cofactors

ID	Name	Formula	Copies
R06	1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone	C9 H12 Cl3 N3 O3	2
MG	Magnesium ion	Mg	2

Water and common crystallization additives (CL, GOL, EDO, ACT) are not listed.

Primary citation

The structure of S. aureus alpha-hemolysin in complex with a bicyclic peptide inhibitor. Whiteside, J.R., Diaz-Saez, L., Rowland, C.E. et al. To be published.

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…
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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