SMTL ID : 8aa2.1

Inactive levan utilisation machinery (utilisome) in the presence of levan fructo-oligosaccharides DP 15-25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

1 x FRU- FRU- FRU- FRU- FRU- FRU- FRU- FRU- FRU- FRU- FRU- FRU- FRU: beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-[beta-D-fructofuranose-(2-1)]beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose

FRU-FRU-FRU-FRU-FRU-FRU-FRU-FRU-FRU-FRU-FRU-FRU-FRU.1: 20 residues within 4Å: Chain A: W.237, R.239, F.263, D.285, E.294, N.440, E.443, K.445, N.447, Y.457, D.460 Chain C: N.317, N.318, S.319, W.320, W.334, N.371, T.373, Q.375, W.382 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.285

2 x FRU- FRU- FRU- FRU- FRU: beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose

FRU-FRU-FRU-FRU-FRU.2: 19 residues within 4Å: Chain A: D.81, N.85, Y.90, H.91, I.123, G.124, T.125, N.144, Q.155, N.186, D.187, R.189, D.190, E.242, C.243, Q.260, R.265, E.335, W.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.85, A:Y.90, A:W.338 FRU-FRU-FRU-FRU-FRU.3: 18 residues within 4Å: Chain D: D.81, N.85, Y.90, H.91, I.123, G.124, T.125, N.144, N.186, D.187, R.189, E.242, C.243, Q.260, R.265, Y.303, E.335, W.338 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.85, D:Y.90, D:W.338

2 x FRU- FRU- FRU- FRU- FRU- FRU- FRU: beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-[beta-D-fructofuranose-(2-1)]beta-D-fructofuranose-(2-6)-beta-D-fructofuranose

FRU-FRU-FRU-FRU-FRU-FRU-FRU.4: 20 residues within 4Å: Chain E: D.59, I.60, N.61, D.85, G.86, W.103, L.308, C.316, F.319, R.386, Y.413 Chain F: E.404, T.405, D.408, D.431, R.432, F.674, Q.677, N.926, V.927 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.408, F:D.408, F:R.432 FRU-FRU-FRU-FRU-FRU-FRU-FRU.6: 18 residues within 4Å: Chain G: D.59, N.61, D.85, G.86, W.103, L.308, C.316, F.319, R.386, Y.413 Chain H: E.404, T.405, D.408, D.431, R.432, F.674, N.926, V.927 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.408, H:R.432

2 x FRU- FRU- FRU- FRU: beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose-(2-6)-beta-D-fructofuranose

FRU-FRU-FRU-FRU.5: 9 residues within 4Å: Chain F: A.191, G.192, H.194, E.195, Q.397, Y.447, K.479, E.506, W.508 No protein-ligand interaction detected (PLIP) FRU-FRU-FRU-FRU.7: 10 residues within 4Å: Chain H: A.191, G.192, H.194, E.195, Q.397, Y.447, K.479, K.504, E.506, W.508 No protein-ligand interaction detected (PLIP)

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 5 residues within 4Å: Chain E: E.280, Y.291, S.417, N.419 Chain F: N.689 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:E.280, E:E.280, E:Y.291, E:S.417 MG.9: 6 residues within 4Å: Chain F: D.862, D.864, N.866, V.868, D.870, D.873 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.862, F:D.864, F:V.868, F:D.873, F:D.873 MG.10: 5 residues within 4Å: Chain G: E.280, Y.291, S.417, N.419 Chain H: N.689 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:E.280, G:E.280, G:Y.291, G:S.417 MG.11: 6 residues within 4Å: Chain H: D.862, D.864, N.866, V.868, D.870, D.873 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:D.862, H:D.864, H:V.868, H:D.873, H:D.873

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

White, J.B.R. et al., Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes. Nature (2023)

Release Date

2023-06-07

Peptides

Glycoside hydrolase family 32: AD
DUF4960 domain-containing protein: BC
SusD homolog: EG
SusC homolog: FH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
M

B
T

C
G

E
B

G
J

F
A

H
I

Membrane

We predict this structure to be a membrane protein.
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Glycoside hydrolase family 32

DUF4960 domain-containing protein

SusD homolog

SusC homolog

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