SMTL ID : 3fyx.1

The Structure of OmpF porin with a synthetic dibenzo-18-crown-6 as modulator

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-trimer

Ligands

3 x 451: N-(6,7,9,10,17,18,20,21-octahydrodibenzo[b,k][1,4,7,10,13,16]hexaoxacyclooctadecin-2-yl)acetamide(Covalent)

451.1: 14 residues within 4Å: Chain A: G.15, C.16, R.42, R.82, Y.102, D.113, L.115, P.116, E.117, G.119, G.120, A.123, R.132, Q.339 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.123, A:Q.339 Hydrogen bonds: A:R.42, A:R.42, A:R.82, A:R.82, A:R.132, A:Q.339 451.3: 14 residues within 4Å: Chain B: G.15, C.16, R.42, R.82, Y.102, D.113, L.115, P.116, E.117, G.119, G.120, A.123, R.132, Q.339 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.123, B:Q.339 Hydrogen bonds: B:R.42, B:R.42, B:R.82, B:R.82, B:R.132, B:Q.339 451.5: 14 residues within 4Å: Chain C: G.15, C.16, R.42, R.82, Y.102, D.113, L.115, P.116, E.117, G.119, G.120, A.123, R.132, Q.339 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:A.123, C:Q.339 Hydrogen bonds: C:R.42, C:R.42, C:R.82, C:R.82, C:R.132, C:Q.339

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 6 residues within 4Å: Chain A: Y.22, M.38, A.123, Y.124, S.125, R.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125, A:R.167 Salt bridges: A:D.121 EPE.4: 6 residues within 4Å: Chain B: Y.22, M.38, A.123, Y.124, S.125, R.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.125, B:R.167 Salt bridges: B:D.121 EPE.6: 6 residues within 4Å: Chain C: Y.22, M.38, A.123, Y.124, S.125, R.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.125, C:R.167 Salt bridges: C:D.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reitz, S. et al., On the function and structure of synthetically modified porins. Angew.Chem.Int.Ed.Engl. (2009)

Release Date

2009-06-30

Peptides

Outer membrane protein F: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Outer membrane protein F