SMTL ID : 2y2x.2 (1 other biounit)

Crystal Structure of Pseudomonas Aeruginosa OpdK with Vanillate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: H.215, G.225, A.226, N.227, L.252, S.254 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.226, A:S.254 EDO.2: 4 residues within 4Å: Chain A: K.268, G.270, G.271, D.299 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.268, A:G.271, A:D.299 EDO.3: 3 residues within 4Å: Chain A: L.252, Y.263, R.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.306 Water bridges: A:R.306

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

C8E.4: 2 residues within 4Å: Chain A: Q.148, G.183 No protein-ligand interaction detected (PLIP) C8E.5: 4 residues within 4Å: Chain A: Y.307, G.321, V.323, V.346 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.307, A:V.323, A:V.346 C8E.6: 7 residues within 4Å: Chain A: L.43, G.62, L.63, F.64, G.93, R.94, V.95 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.95 C8E.7: 3 residues within 4Å: Chain A: A.211, L.213, L.228 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.228 C8E.8: 4 residues within 4Å: Chain A: N.17, Y.19, W.37, L.382 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.37 C8E.9: 4 residues within 4Å: Chain A: D.116, Y.122, D.124, R.284 3 PLIP interactions: 3 interactions with chain A Water bridges: A:D.124, A:D.124, A:S.282 C8E.10: 6 residues within 4Å: Chain A: V.305, R.306, Y.307, V.323 Ligands: C8E.11, C8E.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.305, A:Y.307, A:V.323 C8E.11: 4 residues within 4Å: Chain A: Y.325, W.342, R.344 Ligands: C8E.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.325, A:R.344 C8E.12: 4 residues within 4Å: Chain A: H.260, F.262, Y.307 Ligands: C8E.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.262, A:Y.307 C8E.13: 3 residues within 4Å: Chain A: A.184, Y.186, L.195 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.186 C8E.14: 4 residues within 4Å: Chain A: Q.39, F.41, F.64, V.66 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.39, A:F.64 C8E.15: 3 residues within 4Å: Chain A: R.94, D.162, M.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.94, A:R.94, A:M.163, A:M.163 C8E.16: 4 residues within 4Å: Chain A: V.249, G.251, L.266, Q.267 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.249 C8E.17: 6 residues within 4Å: Chain A: H.215, L.224, G.225, A.226, F.253, S.254 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.224, A:A.226, A:F.253 C8E.18: 1 residues within 4Å: Chain A: W.222 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.222, A:W.222

2 x VNL: 4-HYDROXY-3-METHOXYBENZOATE(Non-covalent)

VNL.19: 9 residues within 4Å: Chain A: K.44, F.45, D.59, A.60, I.61, K.109, E.112, M.113, L.114 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.44 Hydrogen bonds: A:F.45, A:A.60, A:L.114 Water bridges: A:K.109, A:K.109, A:K.109, A:K.109 Salt bridges: A:K.109 VNL.20: 7 residues within 4Å: Chain A: H.327, K.340, E.341, W.342, R.370, R.371, S.372 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.340 Hydrogen bonds: A:R.370 Water bridges: A:K.340, A:K.340, A:K.340, A:R.371 Salt bridges: A:H.327, A:K.340

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Touw, D.S. et al., Pseudomonas Aeruginosa Opdk with Vanillate. To be Published

Release Date

2011-12-28

Peptides

VANILLATE PORIN OPDK: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Membrane

We predict this structure to be a membrane protein.
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VANILLATE PORIN OPDK

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