1MDT: Monomeric diphtheria toxin

Name: PDB 1MDT: The refined structure of monomeric diphtheria toxin at 2.3 Å resolution
Published: 1994-07-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

The refined structure of monomeric diphtheria toxin at 2.3 Å resolution. Determined by X-ray diffraction at 2.3 Å resolution. Released 31 Jul 1994.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Corynephage beta
Chains: 2
Atoms: 8,524
Mol. weight: 118.13 kDa
Ligands: APU
Released: 31 Jul 1994

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

Secondary structure: helices and β-sheets

1MDT contains 54 α-helices and 64 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: 27 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6-15	10	1
β-strand	18-23	6	1
α-helix	30-33	4
α-helix	48-50	3
β-strand	53-56	4	1
α-helix	59-63	5
β-strand	67	1	2
β-strand	77	1	2
β-strand	79-84	6	1
β-strand	88-94	7	1
α-helix	99-105	7
α-helix	114-117	4
α-helix	121-127	7
β-strand	133-139	7	1
β-strand	147-151	5	1
α-helix	155-158	4
β-strand	160-166	7	1
α-helix	168-170	3
α-helix	176-184	9
α-helix	206-221	16
α-helix	224-231	8
α-helix	240-254	15
α-helix	258-260	3
α-helix	261-267	7
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	3
β-strand	320-321	2	3
α-helix	326-347	22
α-helix	353-357	5
α-helix	359-375	17
α-helix	378-380	3
α-helix	387-388	2
β-strand	389-391	3	4
β-strand	394-398	5	4
α-helix	402-404	3
β-strand	405-407	3	5
β-strand	413-422	10	4
β-strand	427-429	3	6
β-strand	431-435	5	7
β-strand	437	1	4
β-strand	441-443	3	4
β-strand	449-452	4	4
β-strand	455-457	3	4
β-strand	459-464	6	7
β-strand	468-473	6	7
β-strand	477-479	3	6
β-strand	480	1	8
β-strand	483	1	8
β-strand	485-493	9	4
α-helix	498-499	2
β-strand	508-518	11	7
β-strand	521-530	10	7
β-strand	532-534	3	5

Chain B: 27 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	6	1	9
α-helix	8-10	3
β-strand	12-15	4	1
β-strand	18-23	6	1
α-helix	30-33	4
β-strand	53-56	4	1
α-helix	59-62	4
α-helix	63-65	3
β-strand	67	1	10
β-strand	77	1	10
β-strand	79-84	6	1
β-strand	88-93	6	1
β-strand	94	1	9
α-helix	99-105	7
α-helix	114-117	4
α-helix	121-127	7
β-strand	133-139	7	1
β-strand	147-151	5	1
α-helix	155-158	4
β-strand	160-166	7	1
α-helix	167-170	4
α-helix	176-182	7
α-helix	183-186	4
α-helix	206-222	17
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	11
β-strand	320-321	2	11
α-helix	326-347	22
α-helix	354-357	4
α-helix	359-375	17
α-helix	378-380	3
β-strand	389-391	3	12
β-strand	394-398	5	12
α-helix	402-404	3
β-strand	405-407	3	13
β-strand	413-422	10	12
β-strand	427-429	3	14
β-strand	431-435	5	15
β-strand	437	1	12
β-strand	441-443	3	12
β-strand	449-452	4	12
β-strand	455-458	4	12
β-strand	459-464	6	15
β-strand	468-473	6	15
β-strand	477-479	3	14
β-strand	480	1	16
β-strand	483	1	16
β-strand	485-493	9	12
β-strand	508-518	11	15
β-strand	521-530	10	15
β-strand	532-534	3	13

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>1MDT_1 DIPHTHERIA TOXIN (chains A, B)
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	2

Primary citation

Refined structure of monomeric diphtheria toxin at 2.3 A resolution. Bennett, M.J., Eisenberg, D. Protein Sci (1994) 3:1464-1475. 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
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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