SMTL ID : 7nre.1

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x TRP- ASN- UX8- SER- LYS- SER- PHE: Darobactin(Non-covalent)

TRP-ASN-UX8-SER-LYS-SER-PHE.1: 22 residues within 4Å: Chain A: T.24, G.25, S.26, F.27, N.28, F.29, G.30, I.31, G.32, Q.42, V.45, Q.46, Q.47, P.380, L.381, G.382, P.383, I.407, G.408, K.409, T.410, W.411 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.27, A:F.27, A:F.29 Hydrogen bonds: A:G.25, A:F.27, A:F.27, A:N.28, A:F.29, A:F.29, A:I.31, A:G.408 Water bridges: A:W.411, A:W.411

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

C8E.2: 5 residues within 4Å: Chain A: T.80, D.82, V.84, L.116, F.118 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.118 C8E.3: 9 residues within 4Å: Chain A: F.27, F.29, A.43, G.44, V.45, I.59, N.60, G.61, A.70 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.59 C8E.5: 4 residues within 4Å: Chain A: Y.175, V.200, Y.210, L.242 No protein-ligand interaction detected (PLIP) C8E.6: 8 residues within 4Å: Chain A: I.59, A.70, E.71, L.72, L.90, F.91, Y.92, Y.110 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.90, A:Y.92

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 1 residues within 4Å: Chain A: D.98 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.98, H2O.3 MG.7: 3 residues within 4Å: Chain A: D.304, D.305, K.399 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.304, A:D.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaur, H. et al., The antibiotic darobactin mimics a beta-strand to inhibit outer membrane insertase. Nature (2021)

Release Date

2021-04-21

Peptides

Outer membrane protein assembly factor BamA: 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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Outer membrane protein assembly factor BamA

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