SMTL ID : 8vjo.2 (3 other biounits)

Cryo-EM structure of Myxococcus xanthus EncA encapsulin shell loaded with EncD cargo

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-15-mer

Ligands

15 x GLY- LEU- THR- VAL- GLY- SER- LEU- ARG- GLY: Encapsulin nanocompartment cargo protein EncD(Non-covalent)

GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.1: 15 residues within 4Å: Chain A: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, I.54, P.57, D.228, T.246, D.258, M.259 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.39, A:A.42, A:L.46, A:R.49, A:P.57, A:P.57, A:M.259 Hydrogen bonds: A:R.43, A:R.49, A:R.49, A:R.50, A:T.246, A:D.258, A:D.258, A:D.258, A:D.258, A:M.259 Salt bridges: A:D.53, A:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.2: 14 residues within 4Å: Chain B: I.39, A.42, R.43, L.46, R.49, R.50, I.51, D.53, I.54, P.57, D.228, T.246, D.258, M.259 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.42, B:R.43, B:L.46, B:R.49, B:R.50, B:P.57, B:M.259 Hydrogen bonds: B:R.43, B:R.49, B:R.49, B:R.50, B:T.246, B:T.246, B:D.258, B:D.258, B:D.258, B:D.258 Salt bridges: B:D.53, B:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.3: 14 residues within 4Å: Chain C: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, P.57, D.228, T.246, D.258, M.259 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:A.42, C:R.43, C:L.46, C:R.50, C:P.57, C:M.259 Hydrogen bonds: C:R.43, C:R.49, C:R.49, C:R.50, C:T.246, C:T.246, C:D.258, C:D.258, C:D.258, C:D.258 Salt bridges: C:D.53, C:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.4: 15 residues within 4Å: Chain D: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, I.54, P.57, D.228, T.246, D.258, M.259 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.39, D:A.42, D:L.46, D:R.49, D:P.57, D:P.57, D:M.259 Hydrogen bonds: D:R.43, D:R.49, D:R.49, D:R.50, D:T.246, D:D.258, D:D.258, D:D.258, D:D.258 Salt bridges: D:D.53, D:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.5: 14 residues within 4Å: Chain E: I.39, A.42, R.43, L.46, R.49, R.50, I.51, D.53, I.54, P.57, D.228, T.246, D.258, M.259 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:A.42, E:R.43, E:L.46, E:R.49, E:R.50, E:P.57, E:M.259 Hydrogen bonds: E:R.43, E:R.49, E:R.49, E:R.50, E:T.246, E:T.246, E:D.258, E:D.258, E:D.258 Salt bridges: E:D.53, E:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.6: 14 residues within 4Å: Chain F: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, P.57, D.228, T.246, D.258, M.259 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:A.42, F:R.43, F:L.46, F:R.50, F:P.57, F:M.259 Hydrogen bonds: F:R.43, F:R.49, F:R.49, F:R.50, F:T.246, F:T.246, F:D.258, F:D.258, F:D.258, F:D.258, F:M.259 Salt bridges: F:D.53, F:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.7: 15 residues within 4Å: Chain G: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, I.54, P.57, D.228, T.246, D.258, M.259 18 PLIP interactions: 18 interactions with chain G Hydrophobic interactions: G:I.39, G:A.42, G:L.46, G:R.49, G:P.57, G:P.57, G:M.259 Hydrogen bonds: G:R.43, G:R.49, G:R.49, G:R.50, G:T.246, G:D.258, G:D.258, G:D.258, G:D.258 Salt bridges: G:D.53, G:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.8: 14 residues within 4Å: Chain H: I.39, A.42, R.43, L.46, R.49, R.50, I.51, D.53, I.54, P.57, D.228, T.246, D.258, M.259 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:A.42, H:R.43, H:L.46, H:R.49, H:R.50, H:P.57, H:M.259 Hydrogen bonds: H:R.43, H:R.49, H:R.49, H:R.50, H:T.246, H:T.246, H:D.258, H:D.258, H:D.258 Salt bridges: H:D.53, H:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.9: 14 residues within 4Å: Chain I: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, P.57, D.228, T.246, D.258, M.259 19 PLIP interactions: 19 interactions with chain I Hydrophobic interactions: I:A.42, I:R.43, I:L.46, I:R.50, I:P.57, I:M.259 Hydrogen bonds: I:R.43, I:R.49, I:R.49, I:R.50, I:T.246, I:T.246, I:D.258, I:D.258, I:D.258, I:D.258, I:M.259 Salt bridges: I:D.53, I:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.10: 15 residues within 4Å: Chain J: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, I.54, P.57, D.228, T.246, D.258, M.259 17 PLIP interactions: 17 interactions with chain J Hydrophobic interactions: J:I.39, J:A.42, J:L.46, J:R.49, J:P.57, J:P.57, J:M.259 Hydrogen bonds: J:R.43, J:R.49, J:R.49, J:R.50, J:D.258, J:D.258, J:D.258, J:D.258 Salt bridges: J:D.53, J:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.11: 14 residues within 4Å: Chain K: I.39, A.42, R.43, L.46, R.49, R.50, I.51, D.53, I.54, P.57, D.228, T.246, D.258, M.259 20 PLIP interactions: 20 interactions with chain K Hydrophobic interactions: K:A.42, K:R.43, K:L.46, K:R.49, K:R.50, K:P.57, K:M.259 Hydrogen bonds: K:R.43, K:R.49, K:R.49, K:R.50, K:T.246, K:T.246, K:D.258, K:D.258, K:D.258, K:D.258, K:M.259 Salt bridges: K:D.53, K:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.12: 14 residues within 4Å: Chain L: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, P.57, D.228, T.246, D.258, M.259 20 PLIP interactions: 20 interactions with chain L Hydrophobic interactions: L:A.42, L:R.43, L:L.46, L:R.50, L:P.57, L:M.259 Hydrogen bonds: L:R.43, L:R.49, L:R.49, L:R.50, L:T.246, L:T.246, L:T.246, L:D.258, L:D.258, L:D.258, L:D.258, L:D.258 Salt bridges: L:D.53, L:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.13: 15 residues within 4Å: Chain M: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, I.54, P.57, D.228, T.246, D.258, M.259 18 PLIP interactions: 18 interactions with chain M Hydrophobic interactions: M:I.39, M:A.42, M:L.46, M:R.49, M:P.57, M:P.57, M:M.259 Hydrogen bonds: M:R.43, M:R.49, M:R.49, M:R.50, M:D.258, M:D.258, M:D.258, M:D.258, M:M.259 Salt bridges: M:D.53, M:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.14: 14 residues within 4Å: Chain N: I.39, A.42, R.43, L.46, R.49, R.50, I.51, D.53, I.54, P.57, D.228, T.246, D.258, M.259 20 PLIP interactions: 20 interactions with chain N Hydrophobic interactions: N:A.42, N:R.43, N:L.46, N:R.49, N:R.50, N:P.57, N:M.259 Hydrogen bonds: N:R.43, N:R.49, N:R.49, N:R.50, N:T.246, N:T.246, N:D.258, N:D.258, N:D.258, N:D.258, N:M.259 Salt bridges: N:D.53, N:D.228 GLY-LEU-THR-VAL-GLY-SER-LEU-ARG-GLY.15: 14 residues within 4Å: Chain O: I.39, A.42, R.43, L.46, R.49, R.50, I.51, L.52, D.53, P.57, D.228, T.246, D.258, M.259 20 PLIP interactions: 20 interactions with chain O Hydrophobic interactions: O:A.42, O:R.43, O:L.46, O:R.50, O:P.57, O:M.259 Hydrogen bonds: O:R.43, O:R.49, O:R.49, O:R.50, O:T.246, O:T.246, O:T.246, O:D.258, O:D.258, O:D.258, O:D.258, O:D.258 Salt bridges: O:D.53, O:D.228

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eren, E. et al., Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-05-08

Peptides

EncA: ABCDEFGHIJKLMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

EncA

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