3KWV: Protective antigen PA-63

Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers. Determined by X-ray diffraction at 3.1 Å resolution. Released 10 Nov 2010.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Bacillus anthracis
Chains: 6
Atoms: 20,349
Mol. weight: 307.35 kDa
Ligands: CA
Released: 10 Nov 2010

Explore 3KWV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KWV contains 102 α-helices and 168 β-strands across 6 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: 21 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	185-190	6
β-strand	192-196	5	1
β-strand	201-205	5	1
α-helix	208-211	4
α-helix	216-218	3
β-strand	219	1	1
α-helix	235-240	6
α-helix	249-252	4
β-strand	256	1	2
β-strand	262-273	12	3
β-strand	289-292	4	3
β-strand	293-297	5	4
β-strand	328-334	7	4
α-helix	346-350	5
β-strand	358-368	11	3
β-strand	374-375	2	5
β-strand	381-385	5	4
β-strand	389-394	6	4
β-strand	404-405	2	5
β-strand	409-411	3	3
α-helix	417-418	2
β-strand	419-420	2	3
β-strand	432-434	3	3
α-helix	436-445	10
β-strand	447-452	6	4
β-strand	458-463	6	6
β-strand	468-476	9	6
α-helix	477-479	3
α-helix	481-487	7
β-strand	488-493	6	2
β-strand	501-506	6	2
β-strand	508	1	7
α-helix	513-516	4
α-helix	519-520	2
β-strand	522	1	8
α-helix	523-531	9
β-strand	534	1	9
β-strand	541-542	2	9
β-strand	545-546	2	9
α-helix	547-549	3
β-strand	550-554	5	2
α-helix	556-568	13
α-helix	574-576	3
β-strand	582	1	8
β-strand	584	1	7
β-strand	588-593	6	2
β-strand	596-598	3	10
β-strand	604-607	4	10
α-helix	609-616	8
β-strand	626-629	4	11
α-helix	633-636	4
β-strand	639-647	9	12
α-helix	648	1
β-strand	653-655	3	12
β-strand	666-669	4	11
β-strand	673-677	5	11
α-helix	679-681	3
β-strand	696-702	7	12
α-helix	703-705	3
β-strand	724-729	6	12

Chain B: 16 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	185-190	6
β-strand	192-196	5	13
β-strand	201-205	5	13
α-helix	208-214	7
β-strand	219	1	13
α-helix	235-240	6
α-helix	249-252	4
β-strand	256	1	14
β-strand	262-273	12	15
β-strand	289-292	4	15
β-strand	293-297	5	16
β-strand	328-334	7	16
α-helix	346-350	5
β-strand	358-368	11	15
β-strand	374-375	2	17
β-strand	381-385	5	16
β-strand	389-394	6	16
β-strand	404-405	2	17
β-strand	409-411	3	15
α-helix	417-418	2
β-strand	419-420	2	15
β-strand	432-434	3	15
α-helix	436-445	10
β-strand	447-452	6	16
β-strand	458-462	5	18
β-strand	469-476	8	18
α-helix	477-479	3
α-helix	481-487	7
β-strand	488-493	6	14
β-strand	501-506	6	14
β-strand	508	1	19
α-helix	519-520	2
β-strand	522	1	20
α-helix	523-531	9
β-strand	534	1	21
β-strand	541-542	2	21
β-strand	545-546	2	21
α-helix	547-549	3
β-strand	550-554	5	14
α-helix	556-568	13
α-helix	574-576	3
β-strand	582	1	20
β-strand	584	1	19
β-strand	588-593	6	14
β-strand	596-598	3	22
β-strand	604-607	4	22
α-helix	609-617	9
β-strand	619-622	4	23
β-strand	626-629	4	23
β-strand	639-647	9	24
β-strand	653-655	3	24
β-strand	674-677	4	23
β-strand	696-702	7	24
α-helix	703-705	3
β-strand	724-729	6	24

Chain C: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	32-43	12
β-strand	44	1	13
α-helix	51-65	15
α-helix	68-76	9
β-strand	80-84	5	25
α-helix	99-102	4
β-strand	103-105	3	26
β-strand	111-113	3	26
α-helix	114-116	3
β-strand	119-122	4	25
β-strand	128-132	5	25
α-helix	135-138	4
α-helix	141-156	16
α-helix	168-178	11
α-helix	184-189	6
α-helix	200-202	3
α-helix	205-208	4
α-helix	210-225	16
α-helix	227-236	10
α-helix	238-249	12

Chain D: 20 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	185-190	6
β-strand	192-196	5	27
β-strand	201-205	5	27
α-helix	208-211	4
β-strand	219	1	27
α-helix	235-240	6
α-helix	249-252	4
β-strand	256	1	28
β-strand	262-273	12	29
β-strand	289-292	4	29
β-strand	293-297	5	30
β-strand	328-334	7	30
α-helix	346-350	5
β-strand	358-368	11	29
β-strand	374-375	2	31
β-strand	381-385	5	30
β-strand	389-394	6	30
β-strand	404-405	2	31
β-strand	409-411	3	29
α-helix	417-418	2
β-strand	419-420	2	29
β-strand	432-434	3	29
α-helix	436-445	10
β-strand	447-452	6	30
β-strand	458-463	6	32
β-strand	468-476	9	32
α-helix	477-479	3
α-helix	481-487	7
β-strand	488-493	6	28
β-strand	501-506	6	28
β-strand	508	1	33
α-helix	513-516	4
α-helix	519-520	2
β-strand	522	1	34
α-helix	523-531	9
β-strand	534	1	35
β-strand	541-542	2	35
β-strand	545-546	2	35
α-helix	547-549	3
β-strand	550-554	5	28
α-helix	556-568	13
α-helix	574-576	3
β-strand	582	1	34
β-strand	584	1	33
β-strand	588-593	6	28
β-strand	596-598	3	36
β-strand	604-607	4	36
α-helix	609-616	8
β-strand	626-629	4	37
α-helix	633-636	4
β-strand	639-647	9	38
α-helix	648	1
β-strand	653-655	3	38
β-strand	666-669	4	37
β-strand	673-677	5	37
α-helix	679-681	3
β-strand	696-702	7	38
α-helix	703-705	3
β-strand	724-729	6	38

Chain E: 17 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	185-190	6
β-strand	192-196	5	39
β-strand	201-205	5	39
α-helix	208-214	7
β-strand	219	1	39
α-helix	235-240	6
α-helix	249-252	4
β-strand	256	1	40
β-strand	262-273	12	41
β-strand	289-292	4	41
β-strand	293-297	5	42
β-strand	328-334	7	42
α-helix	346-350	5
β-strand	358-368	11	41
β-strand	374-375	2	43
β-strand	381-385	5	42
β-strand	389-394	6	42
β-strand	404-405	2	43
β-strand	409-411	3	41
α-helix	417-418	2
β-strand	419-420	2	41
β-strand	432-434	3	41
α-helix	436-445	10
β-strand	447-452	6	42
β-strand	458-462	5	44
β-strand	469-476	8	44
α-helix	477-479	3
α-helix	481-487	7
β-strand	488-493	6	40
β-strand	501-506	6	40
β-strand	508	1	45
α-helix	515-517	3
α-helix	519-520	2
β-strand	522	1	46
α-helix	523-531	9
β-strand	534	1	47
β-strand	541-542	2	47
β-strand	545-546	2	47
α-helix	547-549	3
β-strand	550-554	5	40
α-helix	556-568	13
α-helix	574-576	3
β-strand	582	1	46
β-strand	584	1	45
β-strand	588-593	6	40
β-strand	596-598	3	48
β-strand	604-607	4	48
α-helix	609-617	9
β-strand	619-622	4	49
β-strand	626-629	4	49
β-strand	639-647	9	50
β-strand	653-655	3	50
β-strand	674-677	4	49
β-strand	696-702	7	50
α-helix	703-705	3
β-strand	724-729	6	50

Chain F: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	32-43	12
β-strand	44	1	39
α-helix	51-65	15
α-helix	68-76	9
β-strand	80-84	5	51
α-helix	99-102	4
β-strand	103-105	3	52
β-strand	111-113	3	52
α-helix	114-116	3
β-strand	119-122	4	51
β-strand	128-132	5	51
α-helix	135-138	4
α-helix	141-156	16
α-helix	168-178	11
α-helix	184-188	5
α-helix	200-202	3
α-helix	205-208	4
α-helix	210-225	16
α-helix	227-236	10
α-helix	238-249	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protective antigen PA-63	A, B, D, E	protein	548	Bacillus anthracis	P13423 (AlphaFold model)
Lethal factor	C, F	protein	263	Bacillus anthracis	P15917 (AlphaFold model)

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

>3KWV_1 Protective antigen PA-63 (chains A, B, D, E)
STSAGPTVPDRDNDGIPDSLEVEGYTVDVKNKRTFLSPWISNIHEKKGLTKYKSSPEKWS
TASDPYSDFEKVTGRIDKNVSPEARHPLVAAYPIVHVDMENIILSKNEDQSTQNTDSQTR
TISKNTSTSRTHTSEPGSNSNSSTVAIDHSLSLAGERTWAETMGLNTADTARLNANIRYV
NTGTAPIYNVLPTTSLVLGKNQTLATIKAKENQLSQILAPNNYYPSKNLAPIALNAQDDF
SSTPITMNYNQFLELEKTKQLRLDTDQVYGNIATYNFENGRVRVDTGSNWSEVLPQIQET
TARIIFNGKDLNLVERRIAAVNPSDPLETTKPDMTLKEALKIAFGFNEPNGNLQYQGKDI
TEFDFNFDQQTSQNIKNQLAELNATNIYTVLDKIKLNAKMNILIRDKRFHYDRNNIAVGA
DESVVKEAHREVINSSTEGLLLNIDKDIRKILSGYIVEIEDTEGLKEVINDRYDMLNISS
LRQDGKTFIDFKKYNDKLPLYISNPNYKVNVYAVTKENTIINPSENGDTSTNGIKKILIF
SKKGYEIG

Sequence of entity 2 (C, F), FASTA

>3KWV_2 Lethal factor (chains C, F)
AGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAE
KLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVY
AKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNA
SDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEA
FNYMDKFNEQEINLSLEELKDQR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8

Primary citation

Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers. Feld, G.K., Thoren, K.L., Kintzer, A.F. et al. Nat Struct Mol Biol (2010) 17:1383-1390. DOI 10.1038/nsmb.1923 · PubMed

Other PDB entries of the same protein (UniProt P13423 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TEW 1.45 Å, Crystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to…
4H2A 1.62 Å, Crystal structure of wild type protective antigen to 1.62 A (pH 7.5)
3MHZ 1.7 Å, 1.7A structure of 2-fluorohistidine labeled Protective Antigen
3TEX 1.7 Å, Crystal Structure of Anthrax Protective Antigen (Membrane Insertion Loop Deleted) to…
4NAM 1.7 Å, 1.7A structure of 5-Fluoro Tryptophan Labeled Protective Antigen (W206Y)
3TEZ 1.83 Å, Crystal Structure of Anthrax Protective Antigen Mutant S337C N664C and dithiolacetone…
4EE2 1.91 Å, Crystal Structure of Anthrax Protective Antigen K446M Mutant to 1.91-A Resolution
5FR3 1.94 Å, X-ray crystal structure of aggregation-resistant protective antigen of Bacillus…
3INO 1.95 Å, 1.95A Resolution Structure of Protective Antigen Domain 4
3Q8B 2.0 Å, Crystal structure of WT Protective Antigen (pH 9.0)
3Q8E 2.1 Å, Crystal structure of Protective Antigen W346F (pH 8.5)
1ACC 2.1 Å, Anthrax protective antigen

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