1TOX: Diphtheria toxin dimer

Name: PDB 1TOX: Diphtheria toxin dimer complexed with NAD
Published: 1996-06-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Diphtheria toxin dimer complexed with NAD. Determined by X-ray diffraction at 2.3 Å resolution. Released 10 Jun 1996.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Corynephage beta
Chains: 2
Atoms: 8,295
Mol. weight: 118.15 kDa
Ligands: NAD
Released: 10 Jun 1996

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

Secondary structure: helices and β-sheets

1TOX contains 55 α-helices and 63 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: 29 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	6	1	1
α-helix	8-10	3
β-strand	12-23	12	2
α-helix	30-33	4
α-helix	48-50	3
β-strand	53-56	4	2
α-helix	59-62	4
α-helix	63-65	3
β-strand	67	1	3
α-helix	75-76	2
β-strand	77	1	3
β-strand	79-93	15	2
β-strand	94	1	1
α-helix	99-105	7
α-helix	114-118	5
α-helix	121-128	8
β-strand	133-139	7	2
β-strand	147-151	5	2
α-helix	155-158	4
β-strand	160-166	7	2
α-helix	176-182	7
α-helix	183-185	3
α-helix	206-221	16
α-helix	224-231	8
α-helix	240-254	15
α-helix	258-260	3
α-helix	261-266	6
α-helix	271-273	3
α-helix	275-288	14
α-helix	291-294	4
α-helix	297-304	8
α-helix	310-314	5
β-strand	316-317	2	4
β-strand	320-321	2	4
α-helix	326-347	22
α-helix	352-357	6
α-helix	359-376	18
α-helix	380-381	2
β-strand	389-391	3	5
β-strand	394-398	5	5
α-helix	402-404	3
β-strand	405-407	3	6
β-strand	412-422	11	5
β-strand	427-428	2	7
β-strand	431-435	5	8
β-strand	437	1	5
β-strand	441-443	3	5
β-strand	449-452	4	5
β-strand	455-458	4	5
β-strand	459-463	5	8
β-strand	468-473	6	8
β-strand	478-479	2	7
β-strand	480	1	9
β-strand	483	1	9
β-strand	484-493	10	5
α-helix	497-499	3
β-strand	508-516	9	8
β-strand	523-530	8	8
β-strand	532-534	3	6

Chain B: 26 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6	1	10
α-helix	8-10	3
β-strand	12-23	12	11
α-helix	30-33	4
β-strand	53-56	4	11
α-helix	59-63	5
β-strand	67	1	12
β-strand	77	1	12
β-strand	79-93	15	11
β-strand	94	1	10
α-helix	99-105	7
α-helix	114-117	4
α-helix	121-128	8
β-strand	133-139	7	11
β-strand	147-151	5	11
α-helix	155-158	4
β-strand	160-166	7	11
α-helix	176-182	7
α-helix	183-185	3
α-helix	206-221	16
α-helix	224-231	8
α-helix	240-254	15
α-helix	258-260	3
α-helix	261-266	6
α-helix	271-273	3
α-helix	275-288	14
α-helix	291-295	5
α-helix	297-304	8
α-helix	310-314	5
β-strand	316-317	2	13
β-strand	320-321	2	13
α-helix	326-347	22
α-helix	352-355	4
α-helix	359-376	18
α-helix	380-381	2
β-strand	389-391	3	14
β-strand	394-398	5	14
α-helix	402-404	3
β-strand	405-407	3	15
β-strand	412-422	11	14
β-strand	427-428	2	16
β-strand	431-435	5	17
β-strand	437	1	18
β-strand	441	1	18
β-strand	442-443	2	14
β-strand	449-452	4	14
β-strand	455-458	4	14
β-strand	459-463	5	17
β-strand	468-473	6	17
β-strand	478-479	2	16
β-strand	480	1	19
β-strand	483	1	19
β-strand	484-493	10	14
α-helix	497-500	4
β-strand	508-516	9	17
β-strand	523-530	8	17
β-strand	532-534	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Diphtheria toxin (dimeric)	A, B	protein	535	Corynephage beta	P00588

Sequence of entity 1 (A, B), FASTA

>1TOX_1 DIPHTHERIA TOXIN (DIMERIC) (chains A, B)
GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKY
DAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGT
EEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYE
YMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSE
EKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT
TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNF
VESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKI
TAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVG
NGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS

Ligands and cofactors

ID	Name	Formula	Copies
NAD	Nicotinamide-adenine-dinucleotide	C21 H27 N7 O14 P2	2

Primary citation

Crystal structure of diphtheria toxin bound to nicotinamide adenine dinucleotide. Bell, C.E., Eisenberg, D. Biochemistry (1996) 35:1137-1149. DOI 10.1021/bi9520848 · PubMed

Other PDB entries of the same protein (UniProt P00588), best resolution first:

1F0L 1.55 Å, 1.55 Å crystal structure of wild type diphtheria toxin
4AE0 2.0 Å, Crystal structure of diphtheria toxin mutant CRM197
1DDT 2.0 Å, The refined structure of dimeric diphtheria toxin at 2.0 Å resolution
4AE1 2.08 Å, Crystal structure of diphtheria toxin mutant CRM197 in complex with nicotinamide
1MDT 2.3 Å, The refined structure of monomeric diphtheria toxin at 2.3 Å resolution
1SGK 2.3 Å, Nucleotide-free diphtheria toxin
1DTP 2.5 Å, The structure of the isolated catalytic domain of diphtheria toxin
1XDT 2.65 Å, Complex of diphtheria toxin and heparin-binding epidermal growth factor
4OW6 2.8 Å, Crystal structure of Diphtheria Toxin at acidic pH

Browse structure collections

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