SMTL ID : 4lse.1

Ion selectivity of OmpF porin soaked in 0.2M NaBr

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

8 x BR: BROMIDE ION(Non-covalent)

BR.1: 2 residues within 4Å: Chain A: Y.15, K.17 Ligand excluded by PLIP BR.2: 3 residues within 4Å: Chain A: M.39, Q.67, N.69 Ligand excluded by PLIP BR.3: 3 residues within 4Å: Chain A: S.126, R.168 Ligands: PEG.7 Ligand excluded by PLIP BR.4: 4 residues within 4Å: Chain A: L.21, M.39, T.40, Y.41 Ligand excluded by PLIP BR.9: 5 residues within 4Å: Chain A: D.127, R.169 Chain B: S.71, E.72, G.73 Ligand excluded by PLIP BR.10: 3 residues within 4Å: Chain B: Y.15, K.17, R.43 Ligand excluded by PLIP BR.14: 6 residues within 4Å: Chain B: F.46, W.62 Chain C: K.17, A.18, A.42, R.43 Ligand excluded by PLIP BR.17: 3 residues within 4Å: Chain C: Y.15, G.16, K.17 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.5: 2 residues within 4Å: Chain A: E.118 Ligands: PEG.7 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: N.208, N.237, N.253 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.208 MG.11: 1 residues within 4Å: Ligands: PEG.12 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain B: N.208, N.237, N.253 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:N.208, H2O.11, H2O.12, H2O.13 MG.16: 3 residues within 4Å: Chain C: N.208, N.237, N.253 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:N.208, H2O.21, H2O.21 MG.18: 4 residues within 4Å: Chain C: D.127, N.162, R.169, N.171 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:R.169, H2O.24, H2O.24

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 4 residues within 4Å: Chain A: Y.33, D.122 Ligands: BR.3, MG.5 No protein-ligand interaction detected (PLIP) PEG.12: 4 residues within 4Å: Chain B: Y.33, G.120, D.122 Ligands: MG.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.33 Water bridges: B:S.126 PEG.19: 8 residues within 4Å: Chain C: T.166, A.167, R.168, Q.204, P.240, S.249, G.250, F.251 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.167, C:R.168, C:G.250, C:G.250 PEG.20: 5 residues within 4Å: Chain C: Y.23, Y.33, G.34, E.118, F.119 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.118 Water bridges: C:Y.33

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

C8E.8: 6 residues within 4Å: Chain A: L.228, A.229, L.260, V.261, A.262, Y.276 No protein-ligand interaction detected (PLIP) C8E.13: 7 residues within 4Å: Chain B: V.175, G.176, G.177, S.178, G.190, A.191, Y.192 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dhakshnamoorthy, B. et al., A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J.Am.Chem.Soc. (2013)

Release Date

2013-10-23

Peptides

Outer membrane protein F: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Outer membrane protein F

Related Entries With Identical Sequence