SMTL ID : 6ofr.1

The crystal structure of the outer membrane transporter YddB from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

7 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 6 residues within 4Å: Chain A: Y.423, L.425, Y.444, Y.446, H.453 Ligands: BOG.6 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.423, A:L.425, A:Y.444 Hydrogen bonds: A:Y.446 Salt bridges: A:H.453 BOG.2: 8 residues within 4Å: Chain A: D.163, W.164, L.165, T.166, A.726, F.754, W.755, L.756 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:A.726, A:F.754, A:L.756, A:L.756 Hydrogen bonds: A:W.164, A:T.166, A:T.166 BOG.3: 7 residues within 4Å: Chain A: A.205, D.206, N.207, F.208, W.252, F.253, A.254 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.208, A:W.252, A:W.252 Hydrogen bonds: A:A.254 BOG.4: 5 residues within 4Å: Chain A: M.523, Y.539, H.574, F.576, K.603 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.539, A:Y.539 Hydrogen bonds: A:K.603, A:K.603 Salt bridges: A:H.574 BOG.5: 4 residues within 4Å: Chain A: Y.196, L.198, R.216, Q.218 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.196, A:L.198 Hydrogen bonds: A:R.216, A:R.216 BOG.6: 6 residues within 4Å: Chain A: F.357, A.379, Y.381, Y.423 Ligands: BOG.1, BOG.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.379, A:Y.423, A:Y.423 BOG.7: 7 residues within 4Å: Chain A: Y.381, Y.383, G.419, D.421, Y.423, N.448 Ligands: BOG.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.383 Hydrogen bonds: A:Y.423

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 2 residues within 4Å: Chain A: L.450, Q.511 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:L.450, A:Q.511, H2O.4, H2O.7, H2O.9 MG.9: 3 residues within 4Å: Chain A: S.162, L.165, S.167 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:L.165, H2O.9, H2O.9

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 11 residues within 4Å: Chain A: I.36, Y.78, L.79, I.80, A.85, Q.108, G.109, Y.110, L.112, I.139, A.141 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:L.79, A:A.85, A:G.109, A:Y.110, A:Y.110, A:I.139, A:A.141 GOL.11: 5 residues within 4Å: Chain A: D.81, R.145, K.249, D.261, D.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.145, A:K.249, A:D.261 GOL.12: 7 residues within 4Å: Chain A: S.84, T.86, N.88, R.133, N.354, I.382, S.384 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.84, A:S.84, A:T.86, A:N.354 Water bridges: A:N.88, A:R.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grinter, R. et al., Protease-associated import systems are widespread in Gram-negative bacteria. Plos Genet. (2019)

Release Date

2019-10-02

Peptides

TonB-dependent outer membrane receptor: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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TonB-dependent outer membrane receptor