SMTL ID : 4pl0.1

Crystal structure of the antibacterial peptide ABC transporter McjD in an outward occluded state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 24 residues within 4Å: Chain A: Y.354, I.360, P.379, S.380, G.381, S.382, G.383, K.384, S.385, T.386, Q.426, E.506, H.537 Chain B: V.463, N.464, N.479, N.480, Y.481, S.482, G.483, G.484, Q.485, A.510 Ligands: MG.2 23 PLIP interactions: 16 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:G.381, A:S.382, A:G.383, A:K.384, A:K.384, A:K.384, A:K.384, A:S.385, A:S.385, A:T.386, A:T.386, A:Q.426, A:Q.426, B:N.464, B:N.464, B:N.479, B:S.482, B:G.484, B:Q.485, B:Q.485 Salt bridges: A:K.389 pi-Stacking: A:Y.354, A:Y.354 ANP.4: 23 residues within 4Å: Chain A: V.463, N.464, N.479, N.480, S.482, G.483, G.484, Q.485, A.510 Chain B: Y.354, I.360, P.379, S.380, G.381, S.382, G.383, K.384, S.385, T.386, Q.426, E.506, H.537 Ligands: MG.5 22 PLIP interactions: 6 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:N.464, A:N.479, A:S.482, A:G.484, A:Q.485, A:Q.485, B:G.381, B:G.381, B:S.382, B:G.383, B:K.384, B:K.384, B:K.384, B:K.384, B:S.385, B:S.385, B:T.386, B:T.386, B:Q.426 Salt bridges: B:K.389 pi-Stacking: B:Y.354, B:Y.354

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.385, Q.426, D.505 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.385 MG.5: 4 residues within 4Å: Chain B: S.385, Q.426, D.505 Ligands: ANP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.385

2 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.3: 14 residues within 4Å: Chain A: S.42, P.43, L.46, Y.72, I.287, T.290, S.291, I.294, L.295 Chain B: L.46, I.49, A.69, Y.72 Ligands: BNG.6 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:I.49, B:A.69, B:Y.72, B:Y.72, A:I.287, A:I.287 BNG.6: 13 residues within 4Å: Chain A: L.46, I.49, Y.72 Chain B: S.42, L.46, I.49, T.50, Y.72, I.287, S.291, I.294, L.295 Ligands: BNG.3 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.46, A:L.46, A:I.49, B:L.46, B:I.49, B:I.287 Hydrogen bonds: A:Y.72, A:Y.72, B:S.42

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choudhury, H.G. et al., Structure of an antibacterial peptide ATP-binding cassette transporter in a novel outward occluded state. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-06-18

Peptides

Microcin-J25 export ATP-binding/permease protein McjD: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Microcin-J25 export ATP-binding/permease protein McjD

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