8VJN: Myxococcus xanthus encapsulin cargo protein EncD

Myxococcus xanthus encapsulin cargo protein EncD in complex with flavin mononucleotide. Determined by X-ray diffraction at 2.31 Å resolution. Released 8 May 2024.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Myxococcus xanthus
Chains: 4
Atoms: 1,806
Mol. weight: 31.48 kDa
Ligands: FMN
Released: 8 May 2024

Explore 8VJN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VJN contains 9 α-helices and 0 β-strands across 4 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.

Chains A and C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-28	18
α-helix	34-58	25

Chain B: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	11-28	18
α-helix	34-57	24

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	11-27	17
α-helix	28-30	3
α-helix	34-58	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Encapsulin nanocompartment cargo protein EncD	A, B, C, D	protein	66	Myxococcus xanthus	Q1D9P3 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8VJN_1 Encapsulin nanocompartment cargo protein EncD (chains A, B, C, D)
MHHHHHHMAKNSNPSAFDRDFGYLMPFLDRVAAAASDLEDASARAELTRLMVEEKARWQR
IQELLG

Ligands and cofactors

ID	Name	Formula	Copies
FMN	Flavin mononucleotide	C17 H21 N4 O9 P	2

Primary citation

Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity. Eren, E., Watts, N.R., Conway, J.F. et al. Proc Natl Acad Sci U S A (2024) 121:e2400426121-e2400426121. DOI 10.1073/pnas.2400426121 · PubMed

Other PDB entries of the same protein (UniProt Q1D9P3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8VJO 2.4 Å, Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo

Browse structure collections

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