SMTL ID : 5ofr.1

Structure of the antibacterial peptide ABC transporter McjD in a high energy outward occluded intermediate state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 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 Chain B: V.463, N.479, N.480, S.482, Q.485 Ligands: MG.2, VO4.3 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:P.379, A:G.381, A:G.381, A:S.382, A:G.383, A:K.384, A:S.385, A:T.386, A:T.386, A:Y.395, B:S.482, B:Q.485, B:Q.485 Salt bridges: A:K.384, A:K.389 pi-Stacking: A:Y.354, A:Y.354 ADP.4: 20 residues within 4Å: Chain A: V.463, N.464, N.479, N.480, Y.481, S.482, Q.485 Chain B: Y.354, I.360, P.379, S.380, G.381, S.382, G.383, K.384, S.385, T.386, Y.395 Ligands: MG.5, VO4.6 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:N.464, A:S.482, A:Q.485, A:Q.485, B:G.381, B:G.381, B:S.382, B:G.383, B:K.384, B:S.385, B:T.386 Salt bridges: B:K.384, B:K.389 pi-Stacking: B:Y.354, B:Y.354

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.385, Q.426, D.505 Ligands: ADP.1, VO4.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.385 MG.5: 5 residues within 4Å: Chain B: S.385, Q.426, D.505 Ligands: ADP.4, VO4.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.385

2 x VO4: VANADATE ION(Non-covalent)

VO4.3: 13 residues within 4Å: Chain A: S.380, K.384, S.385, Q.426, D.505, E.506, H.537 Chain B: S.482, G.483, G.484, A.510 Ligands: ADP.1, MG.2 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.384, A:K.384, A:Q.426, A:E.506, B:S.482, B:G.484 VO4.6: 12 residues within 4Å: Chain A: S.482, G.483, G.484, A.510 Chain B: S.380, K.384, S.385, Q.426, E.506, H.537 Ligands: ADP.4, MG.5 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.384, B:Q.426, B:E.506, B:H.537, A:S.482, A:G.484

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bountra, K. et al., Structural basis for antibacterial peptide self-immunity by the bacterial ABC transporter McjD. EMBO J. (2017)

Release Date

2017-09-06

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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