4AE1: Diphtheria toxin mutant CRM197

Name: PDB 4AE1: Crystal structure of diphtheria toxin mutant CRM197 in complex with nicotinamide
Published: 2012-03-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Crystal structure of diphtheria toxin mutant CRM197 in complex with nicotinamide. Determined by X-ray diffraction at 2.08 Å resolution. Released 28 Mar 2012.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: CORYNEBACTERIUM DIPHTHERIAE
Chains: 2
Atoms: 7,722
Mol. weight: 117.21 kDa
Ligands: NCA
Released: 28 Mar 2012

Explore 4AE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4AE1 contains 50 α-helices and 67 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: 26 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	31-33	3
β-strand	53-56	4	2
α-helix	59-63	5
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	153-156	4
β-strand	160-166	7	2
α-helix	176-182	7
α-helix	183-186	4
α-helix	206-220	15
α-helix	224-231	8
α-helix	240-255	16
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	297-305	9
α-helix	310-314	5
β-strand	316-317	2	4
β-strand	320-321	2	4
α-helix	326-347	22
α-helix	355-357	3
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	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	459-464	6	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
β-strand	508-515	8	8
β-strand	524-530	7	8
β-strand	532-534	3	6

Chain B: 24 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	11
α-helix	8-10	3
β-strand	12-23	12	12
α-helix	28-31	4
β-strand	53-56	4	12
α-helix	59-63	5
β-strand	67	1	13
β-strand	77	1	13
β-strand	79-93	15	12
β-strand	94	1	11
α-helix	99-105	7
α-helix	115-118	4
α-helix	121-127	7
β-strand	133-139	7	12
β-strand	147-151	5	12
α-helix	153-156	4
β-strand	160-166	7	12
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	311-314	4
β-strand	316-317	2	14
β-strand	320-321	2	14
α-helix	326-347	22
α-helix	359-376	18
α-helix	380-381	2
β-strand	384	1	15
β-strand	389-391	3	16
β-strand	394-398	5	16
α-helix	401-404	4
β-strand	405-407	3	17
β-strand	412-422	11	16
β-strand	427-428	2	18
β-strand	431-435	5	15
β-strand	437	1	19
β-strand	441	1	19
β-strand	442-443	2	16
β-strand	449-452	4	16
β-strand	455-458	4	16
β-strand	459-463	5	15
β-strand	468-473	6	15
β-strand	478-479	2	18
β-strand	480	1	20
β-strand	483	1	20
β-strand	485-493	9	16
α-helix	498-500	3
β-strand	508-515	8	15
β-strand	524-530	7	15
β-strand	532-534	3	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Diphtheria toxin	A, B	protein	535	CORYNEBACTERIUM DIPHTHERIAE	P00588

Sequence of entity 1 (A, B), FASTA

>4AE1_1 DIPHTHERIA TOXIN (chains A, B)
GADDVVDSSKSFVMENFSSYHGTKPGYVDSIQKGIQKPKSGTQGNYDDDWKEFYSTDNKY
DAAGYSVDNENPLSGKAGGVVKVTYPGLTKVLALKVDNAETIKKELGLSLTEPLMEQVGT
EEFIKRFGDGASRVVLSLPFAEGSSSVEYINNWEQAKALSVELEINFETRGKRGQDAMYE
YMAQACAGNRVRRSVGSSLSCINLDWDVIRDKTKTKIESLKEHGPIKNKMSESPNKTVSE
EKAKQYLEEFHQTALEHPELSELKTVTGTNPVFAGANYAAWAVNVAQVIDSETADNLEKT
TAALSILPGIGSVMGIADGAVHHNTEEIVAQSIALSSLMVAQAIPLVGELVDIGFAAYNF
VESIINLFQVVHNSYNRPAYSPGHKTQPFLHDGYAVSWNTVEDSIIRTGFQGESGHDIKI
TAENTPLPIAGVLLPTIPGKLDVNKSKTHISVNGRKIRMRCRAIDGDVTFCRPKSPVYVG
NGVHANLHVAFHRSSSEKIHSNEISSDSIGVLGYQKTVDHTKVNSKLSLFFEIKS

Ligands and cofactors

ID	Name	Formula	Copies
NCA	Nicotinamide	C6 H6 N2 O	2

Primary citation

Structural Basis for Lack of Toxicity of the Diphtheria Toxin Mutant Crm197. Malito, E., Bursulaya, B., Chen, C. et al. Proc Natl Acad Sci U S A (2012) 109:5229. DOI 10.1073/PNAS.1201964109 · 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
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

Browse structure collections

About this viewer

MolViewer shows 4AE1 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.