SMTL ID : 4gey.1

High pH structure of Pseudomonas putida OprB

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 9 residues within 4Å: Chain A: R.98, E.121, V.122, W.123, G.124, R.125, N.185, W.186, P.187 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.98, A:R.98, A:E.121, A:E.121, A:V.122, A:W.123, A:R.125, A:N.185, A:N.185 Salt bridges: A:R.98, A:R.125

8 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.2: 6 residues within 4Å: Chain A: V.205, Q.206, V.207, M.237, E.238, W.291 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.291 C8E.3: 8 residues within 4Å: Chain A: F.340, L.394, P.408, N.409, L.410, A.428, G.429 Ligands: C8E.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.410, A:A.428 C8E.4: 3 residues within 4Å: Chain A: Y.396, F.398 Ligands: C8E.3 No protein-ligand interaction detected (PLIP) C8E.5: 5 residues within 4Å: Chain A: A.392, L.394, L.410, Y.412, L.426 No protein-ligand interaction detected (PLIP) C8E.6: 5 residues within 4Å: Chain A: W.86, I.136, Q.138, Y.140, V.147 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.86, A:V.147 C8E.7: 4 residues within 4Å: Chain A: Y.48, Y.68 Ligands: C8E.8, DMU.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.68, A:Y.68 C8E.8: 5 residues within 4Å: Chain A: Y.48, D.70, F.72, S.99 Ligands: C8E.7 No protein-ligand interaction detected (PLIP) C8E.9: 2 residues within 4Å: Chain A: Y.252, Q.297 No protein-ligand interaction detected (PLIP)

4 x DMU: DECYL-BETA-D-MALTOPYRANOSIDE(Non-covalent)

DMU.10: 2 residues within 4Å: Chain A: K.414, N.424 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.414, A:N.424 Water bridges: A:S.415, A:D.420 Salt bridges: A:K.414 DMU.11: 7 residues within 4Å: Chain A: R.387, Y.390, A.392, Y.412, K.414, D.420, E.421 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.390, A:Y.390, A:Y.390, A:A.392, A:Y.412, A:K.414 Hydrogen bonds: A:D.420, A:E.421 Water bridges: A:R.387, A:R.387, A:R.387, A:R.387 Salt bridges: A:R.387, A:K.414 DMU.12: 3 residues within 4Å: Chain A: Y.140, F.141, D.142 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.140 Hydrogen bonds: A:F.141, A:D.142 DMU.13: 7 residues within 4Å: Chain A: V.52, T.65, A.66, R.67, Y.68, R.101 Ligands: C8E.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.52, A:Y.68 Hydrogen bonds: A:T.65, A:A.66, A:R.67, A:R.101, A:R.101 Water bridges: A:R.107 Salt bridges: A:R.101

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.14: 2 residues within 4Å: Chain A: H.302, Y.336 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.303, A:Y.336 Salt bridges: A:H.302

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

van den Berg, B., Structural basis for outer membrane sugar uptake in pseudomonads. J.Biol.Chem. (2012)

Release Date

2012-10-24

Peptides

Porin B: 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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Porin B