1PWU: Anthrax Lethal Factor

Crystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases. Determined by X-ray diffraction at 2.7 Å resolution. Released 3 Feb 2004.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Bacillus anthracis
Chains: 2
Atoms: 12,238
Mol. weight: 181.57 kDa
Ligands: GM6, ZN
Released: 3 Feb 2004

Explore 1PWU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1PWU contains 95 α-helices and 50 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: 47 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	31-43	13
β-strand	44-47	4	1
α-helix	54-63	10
α-helix	68-76	9
β-strand	80-84	5	1
α-helix	93-96	4
β-strand	103-105	3	2
β-strand	111-113	3	2
α-helix	114-116	3
β-strand	119-122	4	1
β-strand	128-132	5	1
α-helix	136-138	3
α-helix	141-153	13
α-helix	154-159	6
α-helix	160-163	4
α-helix	168-179	12
α-helix	184-189	6
α-helix	192-195	4
α-helix	203-208	6
α-helix	210-225	16
α-helix	230-236	7
α-helix	238-246	9
α-helix	247-251	5
α-helix	252-261	10
α-helix	264-283	20
α-helix	287-295	9
α-helix	299	1
β-strand	300	1	3
α-helix	301-302	2
α-helix	304-309	6
α-helix	315-319	5
α-helix	324-326	3
α-helix	332-342	11
α-helix	351-360	10
α-helix	370-382	13
β-strand	386	1	3
α-helix	388-395	8
α-helix	406-422	17
β-strand	426	1	4
β-strand	429	1	5
β-strand	432	1	5
β-strand	436-441	6	6
α-helix	443-445	3
α-helix	448-451	4
β-strand	455	1	7
β-strand	463	1	7
α-helix	465-472	8
β-strand	477-480	4	6
β-strand	485-487	3	6
α-helix	492-494	3
β-strand	499-504	6	6
β-strand	510	1	4
β-strand	511-514	4	6
β-strand	518-521	4	6
α-helix	522	1
β-strand	525-537	13	6
β-strand	540-550	11	6
α-helix	552-574	23
β-strand	583-586	4	8
α-helix	592-607	16
α-helix	612-624	13
β-strand	629-632	4	8
α-helix	636-638	3
α-helix	640-643	4
α-helix	649-651	3
β-strand	657-660	4	8
β-strand	665-669	5	8
α-helix	680-700	21
α-helix	712-718	7
α-helix	727-731	5
α-helix	733-743	11
α-helix	749-758	10
α-helix	760-774	15

Chain B: 48 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	34-42	9
β-strand	44-45	2	9
α-helix	54-63	10
α-helix	68-76	9
β-strand	81-84	4	9
α-helix	88-90	3
α-helix	99-102	4
β-strand	103-105	3	10
β-strand	111-113	3	10
β-strand	119-122	4	9
β-strand	128-132	5	9
α-helix	141-153	13
α-helix	154-159	6
α-helix	160-163	4
α-helix	168-178	11
α-helix	184-189	6
α-helix	192-195	4
α-helix	200-202	3
α-helix	203-208	6
α-helix	210-225	16
α-helix	227-236	10
α-helix	238-246	9
α-helix	247-251	5
α-helix	252-260	9
α-helix	264-277	14
α-helix	279-284	6
α-helix	287-297	11
α-helix	299	1
β-strand	300	1	11
α-helix	301-303	3
α-helix	304-308	5
α-helix	313-321	9
α-helix	324-326	3
α-helix	332-346	15
α-helix	350-356	7
α-helix	370-382	13
β-strand	386	1	11
α-helix	388-395	8
α-helix	406-422	17
β-strand	426	1	12
β-strand	436-442	7	13
α-helix	444-451	8
β-strand	455	1	14
β-strand	463	1	14
α-helix	465-473	9
β-strand	477-480	4	13
β-strand	485-487	3	13
α-helix	492-494	3
β-strand	497-504	8	13
β-strand	510	1	12
β-strand	511-514	4	13
β-strand	518-521	4	13
β-strand	525-537	13	13
β-strand	540-550	11	13
α-helix	552-573	22
α-helix	576-577	2
β-strand	583-586	4	15
α-helix	592-608	17
α-helix	612-624	13
β-strand	629-632	4	15
α-helix	636-638	3
α-helix	640-643	4
α-helix	649-651	3
β-strand	657-660	4	15
β-strand	665-669	5	15
α-helix	680-699	20
α-helix	708-710	3
α-helix	712-721	10
α-helix	728-731	4
α-helix	733-744	12
α-helix	749-758	10
α-helix	760-774	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lethal factor	A, B	protein	776	Bacillus anthracis	P15917 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1PWU_1 Lethal factor (chains A, B)
AGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAE
KLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVY
AKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNA
SDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEA
FNYMDKFNEQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPI
EPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRI
QVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNID
ALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSIS
SNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEK
EYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAY
LILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYV
PESRSILLHGPSKGVELRNDSEGFIHCFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKE
EGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS

Ligands and cofactors

ID	Name	Formula	Copies
GM6	3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-trp-methylamide	C20 H28 N4 O4	2
ZN	Zinc ion	Zn	2

Primary citation

The structural basis for substrate and inhibitor selectivity of the anthrax lethal factor. Turk, B.E., Wong, T.Y., Schwarzenbacher, R. et al. Nat Struct Mol Biol (2004) 11:60-66. DOI 10.1038/nsmb708 · PubMed

Other PDB entries of the same protein (UniProt P15917 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4DV8 1.63 Å, Anthrax Lethal Factor metalloproteinase in complex with the Hydroxamic acid based small…
4PKW 1.75 Å, Anthrax toxin lethal factor with bound small molecule inhibitor GM6001
5D1S 2.1 Å, Anthrax toxin lethal factor with hydroxamic acid inhibitor
4PKQ 2.2 Å, Anthrax toxin lethal factor with bound zinc
4PKR 2.2 Å, Anthrax toxin lethal factor with bound small molecule inhibitor 10
5D1T 2.2 Å, Anthrax toxin lethal factor with hydroxamic acid inhibitor
1J7N 2.3 Å, Anthrax Toxin Lethal factor
1YQY 2.3 Å, Structure of B. Anthrax Lethal factor in complex with a hydroxamate inhibitor
4PKS 2.3 Å, Anthrax toxin lethal factor with bound small molecule inhibitor 11
4XM6 2.35 Å, Anthrax toxin lethal factor with ligand-induced binding pocket
4PKT 2.4 Å, Anthrax toxin lethal factor with bound small molecule inhibitor 13
4PKU 2.4 Å, Anthrax toxin lethal factor with bound small molecule inhibitor 15

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