2PFU: Biopolymer transport exbD protein

NMR structure determination of the periplasmic domain of ExbD from E.coli. Determined by solution NMR. Released 23 Oct 2007.

Method: Solution NMR
Organism: Escherichia coli
Chains: 1
Atoms: 761
Mol. weight: 10.91 kDa
Released: 23 Oct 2007

Explore 2PFU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PFU contains 2 α-helices and 5 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: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	65-69	5	1
β-strand	73-76	4	1
β-strand	79-81	3	1
α-helix	86-93	8
β-strand	102-106	5	1
α-helix	112-124	13
β-strand	130-131	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Biopolymer transport exbD protein	A	protein	99	Escherichia coli	P0ABV2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PFU_1 Biopolymer transport exbD protein (chains A)
MDVKVNLPASTSTPQPRPEKPVYLSVKADNSMFIGNDPVTDETMITALNALTEGKKDTTI
FFRADKTVDYETLMKVMDTLHQAGYLKIGLVGEETAKAK

Primary citation

The solution structure of the periplasmic domain of the TonB system ExbD protein reveals an unexpected structural homology with siderophore-binding proteins. Garcia-Herrero, A., Peacock, R.S., Howard, S.P. et al. Mol Microbiol (2007) 66:872-889. DOI 10.1111/j.1365-2958.2007.05957.x · PubMed

Other PDB entries of the same protein (UniProt P0ABV2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VGC 1.42 Å, Complex of ExbD with D-box peptide: Orthorhombic form
8VGD 1.42 Å, Complex of ExbD with D-box peptide: Tetragonal form
8P9R 1.52 Å, Structure of the periplasmic domain of ExbD from E. coli in complex with TonB
9DDO 2.8 Å, E. coli TonB-ExbBD TonB bound to ExbB chain C
9DDP 3.16 Å, E. coli TonB-ExbBD TonB bound to ExbB chain E
9DDQ 3.19 Å, E. coli TonB-ExbBD TonB bound to ExbB chain A
6TYI 3.3 Å, ExbB-ExbD complex in MSP1E3D1 nanodisc
5SV1 3.5 Å, Structure of the ExbB/ExbD complex from E. coli at pH 4.5
5ZFU 6.7 Å, Structure of the ExbB/ExbD hexameric complex (ExbB6ExbD3TM)
5ZFV 7.1 Å, Structure of the ExbB/ExbD pentameric complex (ExbB5ExbD1TM)

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