4IDJ: S.Aureus a-hemolysin monomer

S.Aureus a-hemolysin monomer in complex with Fab. Determined by X-ray diffraction at 3.36 Å resolution. Released 26 Jun 2013.

Method: X-ray diffraction
Resolution: 3.36 Å
Organisms: Staphylococcus aureus, Homo sapiens
Chains: 3
Atoms: 5,600
Mol. weight: 83.25 kDa
Released: 26 Jun 2013

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

Secondary structure: helices and β-sheets

4IDJ contains 16 α-helices and 76 β-strands across 3 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, 30 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	1
β-strand	20-29	10	1
β-strand	34-43	10	1
β-strand	50-61	12	1
β-strand	66-70	5	2
β-strand	75-81	7	2
β-strand	83-89	7	3
β-strand	97-102	6	1
β-strand	107	1	4
β-strand	111-118	8	5
β-strand	124-127	4	5
β-strand	145-149	5	5
β-strand	153	1	6
β-strand	155	1	4
β-strand	156-157	2	3
β-strand	164-170	7	3
β-strand	171	1	6
β-strand	174-176	3	7
β-strand	179-182	4	7
β-strand	188	1	2
β-strand	192	1	2
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
β-strand	224	1	1
β-strand	228-235	8	1
β-strand	244-250	7	3
β-strand	253-259	7	2
β-strand	267-274	8	2
β-strand	278-285	8	3
β-strand	290-292	3	3

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	9
β-strand	4-6	3	10
α-helix	7-9	3
β-strand	10	1	11
β-strand	18-24	7	10
β-strand	26	1	9
β-strand	34-39	6	11
β-strand	45-52	8	11
β-strand	56-59	4	11
α-helix	61-63	3
β-strand	67-72	6	10
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	88-95	8	11
α-helix	96	1
β-strand	100H-103	4	11
β-strand	107-109	3	11
β-strand	117	1	12
β-strand	120-124	5	13
β-strand	135-145	11	13
β-strand	146	1	12
β-strand	151-154	4	14
β-strand	163-165	3	13
α-helix	166-167	2
β-strand	176-185	10	13
β-strand	194-200	7	14
α-helix	201-203	3
β-strand	205-211	7	14

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	10-13	4	16
β-strand	15	1	17
β-strand	17	1	17
β-strand	19-24	6	15
β-strand	34-38	5	16
α-helix	43	1
β-strand	44-49	6	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62-63	2	15
β-strand	66-67	2	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	85-89	5	16
β-strand	98	1	16
β-strand	102-106	5	16
β-strand	111	1	18
β-strand	114-118	5	19
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	19
β-strand	140	1	18
β-strand	144-150	7	20
β-strand	153-155	3	20
β-strand	159-163	5	19
α-helix	164-167	4
β-strand	173-182	10	19
α-helix	183-187	5
β-strand	191-198	8	20
β-strand	201-210	10	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-hemolysin	A	protein	295	Staphylococcus aureus	P09616 (AlphaFold model)
Fab Heavy chain	H	protein	239	Homo sapiens
Fab Light chain	L	protein	215	Homo sapiens

Sequence of entity 1 (A), FASTA

>4IDJ_1 Alpha-hemolysin (chains A)
GSADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMLKKVFYSFIDDKNHNKKLLVIRTK
GTIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTY
GFNGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQN
WGPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKA
SKQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Sequence of entity 2 (H), FASTA

>4IDJ_2 Fab Heavy chain (chains H)
QVQLVQSGAEVKKPGSSVKVSCKTSGGTFNNVAINWVRQAPGQGLEWMGGIIPGLDTPNY
AQKFQGRVTITADKSTTSTYLELSSLRSDDTAVYYCAREMEVSGRWRPTEAFEIWGQGTM
VTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKAAAHHHHHHHHHH

Sequence of entity 3 (L), FASTA

>4IDJ_3 Fab Light chain (chains L)
ETTLTQSPGTLSLSPGERATLSCRASQTISNNFVAWYQQKPGQAPRLLIYGASTRATGIP
DRFSGSGSGTDFTLTISSLEPEDFAVYYCQQYGSSPYTFGQGTKVDIKRADAAPTVSIFP
PSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTL
TLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Mechanism of Action and In Vivo Efficacy of a Human-Derived Antibody against Staphylococcus aureus alpha-Hemolysin. Foletti, D., Strop, P., Shaughnessy, L. et al. J Mol Biol (2013) 425:1641-1654. DOI 10.1016/j.jmb.2013.02.008 · 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…
4YHD 2.8 Å, Staphylococcal alpha-hemolysin H35A mutant monomer

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