SMTL ID : 8ckd.1

PBP AccA from A. fabrum C58 in complex with agrocinopine D-like

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x Y4H: Agrocinopine D-like (C2-C2 linked; with an alpha and beta-D-glucopyranose)(Non-covalent)

Y4H.1: 22 residues within 4Å: Chain A: N.16, I.24, S.25, N.26, Y.117, W.150, N.256, M.344, Y.347, Y.348, Y.374, G.377, F.379, W.390, S.391, N.392, G.393, W.395, T.402, E.406, E.482 Ligands: Y45.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.26, A:N.26, A:Y.117, A:Y.117, A:N.256, A:Y.347, A:Y.348, A:Y.348, A:Y.348, A:W.390, A:S.391, A:S.391, A:G.393, A:E.406 Water bridges: A:Y.374, A:W.395, A:E.406

1 x Y45: Agrocinopine D-like (C2-C2 linked; with two alpha-D-glucopyranoses)(Non-covalent)

Y45.2: 21 residues within 4Å: Chain A: N.16, I.24, S.25, N.26, Y.117, W.150, M.344, Y.347, Y.348, Y.374, G.377, F.379, W.390, S.391, N.392, G.393, W.395, T.402, E.406, E.482 Ligands: Y4H.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.25, A:N.26, A:N.26, A:Y.117, A:Y.117, A:Y.347, A:Y.347, A:Y.348, A:Y.348, A:W.390, A:S.391, A:S.391, A:G.393, A:E.406 Water bridges: A:Y.374, A:W.395, A:E.406

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: K.161, K.162, L.163, G.164 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.162 EDO.4: 8 residues within 4Å: Chain A: L.222, I.223, S.224, G.225, Y.244, D.246, L.247, R.471 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.246, A:R.471 EDO.5: 4 residues within 4Å: Chain A: N.437, G.438, K.439, E.440 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.439 Water bridges: A:E.440, A:E.440

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morera, S. et al., A highly conserved ligand-binding site for AccA transporters of antibiotic and quorum-sensing regulator in Agrobacterium leads to a different specificity. Biochem.J. (2024)

Release Date

2024-01-24

Peptides

ABC transporter substrate-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ABC transporter substrate-binding protein

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