SMTL ID : 4zec.1

PBP AccA from A. tumefaciens C58 in complex with agrocin 84

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x C84: [(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-N-[9-[(2R,3S,5R)-5-[[[(2R,3S)-4-methyl-2,3-bis(oxidanyl)pentanoyl]amino]-oxidanyl-phosphoryl]oxy-3-oxidanyl-oxolan-2-yl]purin-6-yl]phosphonamidic acid(Non-covalent)

C84.1: 20 residues within 4Å: Chain A: N.13, S.22, N.23, Y.114, W.147, N.253, M.341, Y.344, Y.345, F.376, R.385, W.387, S.388, N.389, G.390, T.399, E.403, R.413, W.414, E.479 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.376 Hydrogen bonds: A:N.23, A:N.23, A:N.253, A:Y.344, A:Y.345, A:Y.345, A:R.385, A:W.387, A:S.388, A:S.388, A:N.389, A:G.390, A:E.403, A:R.413, A:R.413 Water bridges: A:R.385

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 10 residues within 4Å: Chain A: P.136, S.137, Y.138, V.429, T.430, V.431, L.432, P.433, N.434, R.438 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.138 Water bridges: A:Y.138, A:N.434, A:N.434

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: N.318, E.321, R.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.318, A:R.324

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

EDO.4: 4 residues within 4Å: Chain A: N.13, N.167, F.180, A.182 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.13 EDO.5: 4 residues within 4Å: Chain A: V.265, T.334, P.335, W.383 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: K.112, S.113, S.115, N.407 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.407 Water bridges: A:V.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

El Sahili, A. et al., A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens. Plos Pathog. (2015)

Release Date

2015-08-19

Peptides

ABC transporter, substrate binding protein (Agrocinopines A and B): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ABC transporter, substrate binding protein (Agrocinopines A and B)