SMTL ID : 7nrf.1

Crystal structure of E.coli BamA beta-barrel in complex with darobactin (crystal form 2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 21 residues within 4Å: Chain A: 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 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.25, A:G.25, A:F.27, A:F.27, A:F.27, A:F.29, A:F.29, A:I.31, A:I.31, A:K.409

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.1

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

C8E.3: 10 residues within 4Å: Chain A: W.228, F.319, T.321, P.322, T.323, P.324, F.325, I.326, D.328, F.338 No protein-ligand interaction detected (PLIP) C8E.4: 4 residues within 4Å: Chain A: I.222, D.223, W.228, F.319 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.228 C8E.5: 5 residues within 4Å: Chain A: T.112, Y.132, D.169, F.171 Ligands: C8E.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.132, A:F.171 C8E.6: 11 residues within 4Å: Chain A: T.112, D.113, V.114, L.130, G.131, Y.132, F.171, I.202, P.203, G.204 Ligands: C8E.5 No protein-ligand interaction detected (PLIP) C8E.7: 9 residues within 4Å: Chain A: L.130, F.173, V.200, T.201, I.202, P.203, L.242 Ligands: C8E.8, C8E.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.173, A:F.173, A:V.200 C8E.8: 6 residues within 4Å: Chain A: F.173, V.200, Y.210, L.242 Ligands: C8E.7, C8E.9 No protein-ligand interaction detected (PLIP) C8E.9: 4 residues within 4Å: Chain A: I.202, P.203 Ligands: C8E.7, C8E.8 No protein-ligand interaction detected (PLIP) C8E.10: 9 residues within 4Å: Chain A: F.27, F.29, A.43, G.44, V.45, I.59, N.60, G.61, A.70 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.45, A:V.45, A:I.59

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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