1PTO: Pertussis toxin

Name: PDB 1PTO: The structure of a pertussis toxin-sugar complex as a model for receptor binding
Published: 1995-09-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

The structure of a pertussis toxin-sugar complex as a model for receptor binding. Determined by X-ray diffraction at 3.5 Å resolution. Released 15 Sept 1995.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Bordetella pertussis
Chains: 12
Atoms: 14,614
Mol. weight: 212.51 kDa
Released: 15 Sept 1995

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

Secondary structure: helices and β-sheets

1PTO contains 68 α-helices and 138 β-strands across 12 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: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
α-helix	15-21	7
β-strand	23-24	2	2
β-strand	29	1	3
α-helix	32-36	5
α-helix	39-41	3
β-strand	48	1	3
β-strand	50-54	5	1
α-helix	57-77	21
β-strand	83-92	10	1
β-strand	97-99	3	1
α-helix	100-111	12
α-helix	113-115	3
α-helix	119-126	8
β-strand	129-133	5	1
β-strand	135-136	2	2
α-helix	138-140	3
β-strand	141-150	10	1
β-strand	155-159	5	1
α-helix	166-168	3
β-strand	174	1	1
α-helix	177-178	2
α-helix	181-183	3
β-strand	191-193	3	4
β-strand	198-199	2	4
α-helix	200-205	6
β-strand	225-227	3	4
α-helix	228-232	5

Chain B: 9 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	10-12	3
β-strand	13	1	5
β-strand	18	1	6
β-strand	27-29	3	5
α-helix	30-31	2
α-helix	32-37	6
α-helix	39-46	8
β-strand	54-57	4	6
β-strand	60-63	4	6
α-helix	65-67	3
β-strand	70-72	3	6
α-helix	78-81	4
β-strand	85	1	6
β-strand	87-89	3	5
β-strand	91-92	2	7
β-strand	101-114	14	7
β-strand	119-125	7	7
β-strand	128-135	8	7
α-helix	146-155	10
α-helix	156-160	5
β-strand	162-173	12	7
β-strand	184-191	8	7

Chain C: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13	1	8
β-strand	18-19	2	9
β-strand	22	1	9
α-helix	23-24	2
β-strand	27-29	3	8
α-helix	30-31	2
α-helix	32-37	6
α-helix	39-48	10
β-strand	54-56	3	9
β-strand	61-63	3	9
α-helix	65-67	3
β-strand	70-72	3	9
α-helix	79-81	3
β-strand	84-85	2	9
β-strand	87-89	3	8
β-strand	91-93	3	10
β-strand	101-113	13	10
β-strand	119-125	7	10
β-strand	128-135	8	10
α-helix	146-158	13
β-strand	163-173	11	10
β-strand	183-191	9	10

Chain D: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	7
β-strand	17	1	10
β-strand	19-21	3	11
β-strand	24-29	6	11
β-strand	32-36	5	7
α-helix	44-46	3
β-strand	48-51	4	7
β-strand	53-55	3	11
α-helix	63-73	11
β-strand	78-89	12	7
β-strand	92-102	11	7

Chain E: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	12
β-strand	11-20	10	12
β-strand	27-36	10	12
α-helix	44-46	3
β-strand	48-55	8	12
α-helix	63-74	12
β-strand	77-78	2	12
β-strand	81-87	7	12
β-strand	94-97	4	12
β-strand	100-101	2	10
β-strand	102	1	12

Chain F: 2 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-10	6	12
β-strand	11-20	10	7
β-strand	23-31	9	7
β-strand	37-43	7	7
α-helix	52-66	15
β-strand	70-74	5	12
α-helix	83	1
β-strand	84-85	2	7
β-strand	86-91	6	12

Chain G: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	13
α-helix	15-21	7
β-strand	23-24	2	14
β-strand	29	1	15
α-helix	32-36	5
α-helix	39-41	3
β-strand	48	1	15
β-strand	50-54	5	13
α-helix	57-77	21
β-strand	83-92	10	13
β-strand	97-99	3	13
α-helix	100-111	12
α-helix	119-126	8
β-strand	129-133	5	13
β-strand	135-136	2	14
α-helix	138-140	3
β-strand	141-143	3	13
β-strand	146-150	5	13
β-strand	155-159	5	13
α-helix	166-168	3
β-strand	174	1	13
α-helix	177-178	2
α-helix	181-183	3
β-strand	191-193	3	16
β-strand	198-199	2	16
α-helix	200-205	6
β-strand	225-227	3	16
α-helix	228-232	5

Chain H: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
β-strand	13	1	17
β-strand	18	1	18
β-strand	27-29	3	17
α-helix	30-31	2
α-helix	32-37	6
α-helix	39-46	8
β-strand	54-56	3	18
β-strand	61-63	3	18
α-helix	65-67	3
β-strand	70-72	3	18
α-helix	78-81	4
β-strand	85	1	18
β-strand	87-89	3	17
β-strand	91-92	2	19
β-strand	101-114	14	19
β-strand	119-125	7	19
β-strand	128-135	8	19
α-helix	146-159	14
β-strand	162-173	12	19
β-strand	184-191	8	19

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pertussis toxin (subunit S1)	A, G	protein	244	Bordetella pertussis	P04977 (AlphaFold model)
Pertussis toxin	B	protein	196	Bordetella pertussis	P04978 (AlphaFold model)
Pertussis toxin	C, I	protein	196	Bordetella pertussis	P04979 (AlphaFold model)
Pertussis toxin (subunit S4)	D, E, J, K	protein	110	Bordetella pertussis	P0A3R5 (AlphaFold model)
Pertussis toxin (subunit S5)	F, L	protein	98	Bordetella pertussis	P04981
Pertussis toxin (subunit S2)	H	protein	198	Bordetella pertussis	P04978 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>1PTO_1 PERTUSSIS TOXIN (SUBUNIT S1) (chains A, G)
APVTSPAWADDPPATVYRYDSRPPEDVFQNGFTAWGNNDNVLEHLTGRSCQVGSSNSAFV
STSSSRRYTEVYLEHRMQEAVEAERAGRGTGHFIGYIYEVRADNNFYGAASSYFEYVDTY
GDNAGRILAGALATYQSEYLAHRRIPPENIRRVTRVYHNGITGETTTTEYSNARYVSQQT
RANPNPYTSRRSVASIVGTLVRMAPVVGACMARQAESSEAMAAWSERAGEAMVLVYYESI
AYSF

Sequence of entity 2 (B), FASTA

>1PTO_2 PERTUSSIS TOXIN (chains B)
GIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGTYL
GGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVF
VRSGQPVIGACTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDATFET
YALTGISICNPGSSLC

Sequence of entity 3 (C, I), FASTA

>1PTO_3 PERTUSSIS TOXIN (chains C, I)
GIVIPPKALFTQQGGAYGRCPNGTRALTVAELRGNAELQTYLRQITPGWSIYGLYDGTYL
GQAYGGIIKDAPPGAGFIYRETFCITTIYKTGQPAADHYYSKVTATRLLASTNSRLCAVF
VRDGQSVIGACASPYEGRYRDMYDALRRLLYMIYMSGLAVRVHVSKEEQYYDYEDATFQT
YALTGISLCNPAASIC

Sequence of entity 4 (D, E, J, K), FASTA

>1PTO_4 PERTUSSIS TOXIN (SUBUNIT S4) (chains D, E, J, K)
DVPYVLVKTNMVVTSVAMKPYEVTPTRMLVCGIAAKLGAAASSPDAHVPFCFGKDLKRPG
SSPMEVMLRAVFMQQRPLRMFLGPKQLTFEGKPALELIRMVECSGKQDCP

Sequence of entity 5 (F, L), FASTA

>1PTO_5 PERTUSSIS TOXIN (SUBUNIT S5) (chains F, L)
LPTHLYKNFTVQELALKLKGKNQEFCLTAFMSGRSLVRACLSDAGHEHDTWFDTMLGFAI
SAYALKSRIALTVEDSPYPGTPGDLLELQICPLNGYCE

Sequence of entity 6 (H), FASTA

>1PTO_6 PERTUSSIS TOXIN (SUBUNIT S2) (chains H)
TPGIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGT
YLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCA
VFVRSGQPVIGACTSPYDGKYWSMYSRLRKMLYLIYVAGISVRVHVSKEEQYYDYEDATF
ETYALTGISICNPGSSLC

Primary citation

Structure of a pertussis toxin-sugar complex as a model for receptor binding. Stein, P.E., Boodhoo, A., Armstrong, G.D. et al. Nat Struct Biol (1994) 1:591-596. DOI 10.1038/nsb0994-591 · PubMed

Other PDB entries of the same protein (UniProt P04977 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SNE 1.0 Å, Pertussis toxin S1 subunit bound to BaAD
7SKI 1.1 Å, Pertussis toxin in complex with PJ34
7U6Z 1.3 Å, Pertussis toxin E129D NAD
7SKY 1.37 Å, Pertussis toxin S1 bound to NAD+
7SKK 1.65 Å, pertussis toxin in complex with ADPR and Nicotinamide
6RO0 2.13 Å, Crystal structure of genetically detoxified pertussis toxin gdpt.
1BCP 2.7 Å, Binary complex of pertussis toxin and ATP
1PRT 2.9 Å, The crystal structure of pertussis toxin
9MR7 3.56 Å, Genetiocally detoxified pertussis toxin in complex with hu1B7 Fab and hu11E6 Fab

Browse structure collections

About this viewer

MolViewer shows 1PTO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.