1DDT: Dimeric diphtheria toxin

Name: PDB 1DDT: The refined structure of dimeric diphtheria toxin at 2.0 Å resolution
Published: 1994-07-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

The refined structure of dimeric diphtheria toxin at 2.0 Å resolution. Determined by X-ray diffraction at 2.0 Å resolution. Released 31 Jul 1994.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Corynephage beta
Chains: 1
Atoms: 4,469
Mol. weight: 59.06 kDa
Ligands: APU
Released: 31 Jul 1994

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

Secondary structure: helices and β-sheets

1DDT contains 30 α-helices and 34 β-strands across 1 chain. 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: 30 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6	1	1
α-helix	8-10	3
β-strand	12-15	4	2
β-strand	18-23	6	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
β-strand	77	1	3
β-strand	79-84	6	2
β-strand	88-93	6	2
β-strand	94	1	1
α-helix	99-105	7
α-helix	114-118	5
α-helix	121-127	7
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	168-170	3
α-helix	176-182	7
α-helix	183-186	4
α-helix	206-222	17
α-helix	224-232	9
α-helix	240-254	15
α-helix	258-260	3
α-helix	261-266	6
α-helix	271-273	3
α-helix	275-286	12
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	353-357	5
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	427-429	3	7
β-strand	431-435	5	8
β-strand	437	1	9
β-strand	441	1	9
β-strand	442-443	2	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	477-479	3	7
β-strand	480	1	10
β-strand	483	1	10
β-strand	485-493	9	5
α-helix	498-499	2
β-strand	508-516	9	8
α-helix	518-520	3
β-strand	523-530	8	8
β-strand	532-534	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Diphtheria toxin	A	protein	535	Corynephage beta	P00588

Sequence of entity 1 (A), FASTA

>1DDT_1 DIPHTHERIA TOXIN (chains A)
GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKY
DAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGT
EEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYE
YMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSE
EKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT
TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNF
VESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKI
TAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVG
NGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS

Ligands and cofactors

ID	Name	Formula	Copies
APU	Adenylyl-3'-5'-phospho-uridine-3'-monophosphate	C19 H25 N7 O15 P2	1

Primary citation

Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Bennett, M.J., Choe, S., Eisenberg, D. Protein Sci (1994) 3:1444-1463. 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
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
1TOX 2.3 Å, Diphtheria toxin dimer complexed with NAD
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

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1DDT is part of these collections:

Toxins and how they work

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