1DMA: Domain III of pseudomonas aeruginosa exotoxin

Domain III of pseudomonas aeruginosa exotoxin complexed with nicotinamide and AMP. Determined by X-ray diffraction at 2.5 Å resolution. Released 15 Sept 1995.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Pseudomonas aeruginosa
Chains: 2
Atoms: 3,073
Mol. weight: 47.26 kDa
Ligands: AMP, NCA
Released: 15 Sept 1995

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

Secondary structure: helices and β-sheets

1DMA contains 25 α-helices and 24 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: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	408-410	3	1
β-strand	413-415	3	1
α-helix	419-431	13
β-strand	434-443	10	2
α-helix	444-451	8
β-strand	469-472	4	2
α-helix	475-478	4
α-helix	479-481	3
β-strand	483	1	3
β-strand	495	1	3
β-strand	496-504	9	2
α-helix	505-510	6
β-strand	511-513	3	2
α-helix	523-531	9
α-helix	537	1
β-strand	541-545	5	2
α-helix	546	1
β-strand	552-556	5	2
α-helix	558-561	4
β-strand	565-568	4	2
α-helix	571-574	4
α-helix	580-583	4
α-helix	584-586	3
α-helix	589-592	4
α-helix	598-600	3
β-strand	601	1	2
α-helix	604-608	5

Chain B: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	408	1	4
β-strand	415	1	4
α-helix	419-430	12
β-strand	434-443	10	5
α-helix	444-453	10
β-strand	469-471	3	6
β-strand	472	1	5
α-helix	475-478	4
β-strand	496-504	9	5
α-helix	508-510	3
β-strand	511-513	3	6
α-helix	517	1
α-helix	521-531	11
α-helix	537	1
β-strand	541-544	4	6
β-strand	553-556	4	6
α-helix	558-561	4
β-strand	565-568	4	5
β-strand	574	1	7
β-strand	577	1	7
α-helix	584-586	3
α-helix	589-594	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exotoxin a	A, B	protein	214	Pseudomonas aeruginosa	P11439 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1DMA_1 EXOTOXIN A (chains A, B)
FLGDGGDVSFSTRGTQNWTVERLLQAHRQLEERGYVFVGYHGTFLEAAQSIVFGGVRARS
QDLDAIWRGFYIAGDPALAYGYAQDQEPDARGRIRNGALLRVYVPRSSLPGFYRTSLTLA
APEAAGEVERLIGHPLPLRLDAITGPEEEGGRLETILGWPLAERTVVIPSAIPTDPRNVG
GDLDPSSIPDKEQAISALPDYASQPGKPPREDLK

Ligands and cofactors

ID	Name	Formula	Copies
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1
NCA	Nicotinamide	C6 H6 N2 O	2

Primary citation

The crystal structure of Pseudomonas aeruginosa exotoxin domain III with nicotinamide and AMP: conformational differences with the intact exotoxin. Li, M., Dyda, F., Benhar, I. et al. Proc Natl Acad Sci U S A (1995) 92:9308-9312. DOI 10.1073/pnas.92.20.9308 · PubMed

Other PDB entries of the same protein (UniProt P11439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IKP 1.45 Å, Pseudomonas Aeruginosa Exotoxin A, P201Q, W281A mutant
1IKQ 1.62 Å, Pseudomonas Aeruginosa Exotoxin A, wild type
1XK9 2.1 Å, Pseudomanas exotoxin A in complex with the PJ34 inhibitor
1AER 2.3 Å, Domain III of pseudomonas aeruginosa exotoxin complexed with beta-tad
3B82 2.35 Å, Structure of the eEF2-ExoA(E546H)-NAD+ complex
3B78 2.5 Å, Structure of the eEF2-ExoA(R551H)-NAD+ complex
3B8H 2.5 Å, Structure of the eEF2-ExoA(E546A)-NAD+ complex
1ZM9 2.8 Å, Structure of eEF2-ETA in complex with PJ34
1ZM4 2.9 Å, Structure of the eEF2-ETA-bTAD complex
2ZIT 3.0 Å, Structure of the eEF2-ExoA-NAD+ complex
1ZM2 3.07 Å, Structure of ADP-ribosylated eEF2 in complex with catalytic fragment of ETA
1ZM3 3.07 Å, Structure of the apo eEF2-ETA complex

Browse structure collections

About this viewer

MolViewer shows 1DMA 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.