1XDT: Diphtheria toxin

Complex of diphtheria toxin and heparin-binding epidermal growth factor. Determined by X-ray diffraction at 2.65 Å resolution. Released 25 Feb 1998.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Corynebacterium diphtheriae, Homo sapiens
Chains: 2
Atoms: 4,354
Mol. weight: 67.34 kDa
Released: 25 Feb 1998

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

Secondary structure: helices and β-sheets

1XDT contains 30 α-helices and 40 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 R: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	119-121	3	11
β-strand	124	1	12
α-helix	125-127	3
β-strand	129	1	12
β-strand	132-134	3	11
α-helix	135	1
β-strand	138-139	2	13
β-strand	145-146	2	13

Chain T: 28 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	28-31	4
α-helix	48-50	3
β-strand	53-56	4	2
α-helix	59-64	6
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	114-117	4
α-helix	121-126	6
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	176-183	8
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	291-295	5
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	354-357	4
α-helix	359-376	18
α-helix	380-381	2
β-strand	389-391	3	5
β-strand	394-398	5	5
α-helix	401-404	4
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	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	478-479	2	7
β-strand	480	1	10
β-strand	483	1	10
β-strand	485-493	9	5
α-helix	498-500	3
α-helix	501-503	3
β-strand	508-518	11	8
β-strand	521-530	10	8
β-strand	532-534	3	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Diphtheria toxin	T	protein	535	Corynebacterium diphtheriae	P00588
Heparin-binding epidermal growth factor	R	protein	79	Homo sapiens	Q99075 (AlphaFold model)

Sequence of entity 1 (T), FASTA

>1XDT_1 DIPHTHERIA TOXIN (chains T)
GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKGFYSTDNKY
DAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGT
EEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYE
YMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSE
EKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT
TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNF
VESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKI
TAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVG
NGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS

Sequence of entity 2 (R), FASTA

>1XDT_2 HEPARIN-BINDING EPIDERMAL GROWTH FACTOR (chains R)
GSHMRVTLSSKPQALATPNKEEHGKRKKKGKGLGKKRDPCLRKYKDFCIHGECKYVKELR
APSCICHPGYHGERCHGLS

Primary citation

Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor. Louie, G.V., Yang, W., Bowman, M.E. et al. Mol Cell (1997) 1:67-78. DOI 10.1016/S1097-2765(00)80008-8 · 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
1TOX 2.3 Å, Diphtheria toxin dimer complexed with NAD
1DTP 2.5 Å, The structure of the isolated catalytic domain of diphtheria toxin
4OW6 2.8 Å, Crystal structure of Diphtheria Toxin at acidic pH

Browse structure collections

About this viewer

MolViewer shows 1XDT 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.