SMTL ID : 9cs1.1

E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

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

TRP-ASN-UX8-SER-LYS-SER-PHE.1: 12 residues within 4Å: Chain A: T.3, G.4, S.5, F.6, N.7, F.8, G.9, I.10, Q.21, Q.25, Q.26, L.360 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.6, A:F.8, A:F.8 Hydrogen bonds: A:G.4, A:G.4, A:F.6, A:F.6, A:N.7, A:F.8, A:F.8, A:I.10, A:L.360

2 x 4NE: tetrabutylphosphonium(Non-covalent)

4NE.2: 6 residues within 4Å: Chain A: T.195, T.197, V.209, G.211, T.213, W.215 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.197, A:V.209, A:T.213, A:W.215 4NE.3: 7 residues within 4Å: Chain A: W.29, T.32, Y.34, V.53, G.66, G.67, V.93 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.29, A:Y.34, A:V.53, A:V.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walker, M.E. et al., Antibacterial macrocyclic peptides reveal a distinct mode of BamA inhibition. Nat Commun (2025)

Release Date

2025-04-16

Peptides

Outer membrane protein assembly factor BamA: A
Cyclic peptide CP2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Outer membrane protein assembly factor BamA

Cyclic peptide CP2

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