SMTL ID : 6eq8.1 (3 other biounits)

Structure of the periplasmic binding protein (PBP) MelB (Atu4661) in complex with galactinol from agrobacterium fabrum C58

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: R.31, E.136, P.139, K.143, S.144, W.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.31, A:K.143, A:W.145, A:W.145 EDO.2: 3 residues within 4Å: Chain A: N.485, G.486, K.491 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.491 EDO.3: 3 residues within 4Å: Chain A: G.461, D.462, G.463 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.461 EDO.4: 2 residues within 4Å: Chain A: E.478, T.480 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.382 EDO.5: 5 residues within 4Å: Chain A: V.82, G.83, V.84, K.300, Q.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.82, A:Q.302 EDO.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.7: 1 residues within 4Å: Chain A: P.248 No protein-ligand interaction detected (PLIP)

1 x BQZ: galactinol(Non-covalent)

BQZ.8: 15 residues within 4Å: Chain A: W.110, G.111, G.112, I.115, W.317, R.320, N.333, E.335, N.484, Y.487, S.515, D.519, R.533, W.639, E.641 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.111, A:G.112, A:R.320, A:R.320, A:N.333, A:E.335, A:N.484, A:Y.487, A:Y.487, A:S.515, A:R.533, A:R.533, A:E.641 Water bridges: A:D.114, A:S.515, A:D.519, A:D.519 Salt bridges: A:R.533

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: D.458, D.460, D.462, F.464, N.466, N.476 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.458, A:D.462, A:F.464

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

PEG.10: 1 residues within 4Å: Chain A: K.300 No protein-ligand interaction detected (PLIP) PEG.11: 6 residues within 4Å: Chain A: V.322, V.325, E.338, N.339, A.342, S.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.339 PEG.12: 3 residues within 4Å: Chain A: N.27, G.76, N.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.77

1 x P4G: 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE(Non-covalent)

P4G.13: 4 residues within 4Å: Chain A: S.279, R.281, L.661, F.662 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.279 Water bridges: A:R.281

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.14: 5 residues within 4Å: Chain A: S.492, G.496, G.499, Q.500, K.503 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.503 Water bridges: A:G.499

7 x CL: CHLORIDE ION(Non-functional Binders)

CL.15: 5 residues within 4Å: Chain A: P.264, Y.266, M.267, S.279, Y.280 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain A: R.96 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain A: R.96, N.516 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain A: G.359, G.617, P.633, I.634 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: T.254, Y.255 Ligand excluded by PLIP CL.20: 5 residues within 4Å: Chain A: R.96, Y.280, P.282, D.283, L.314 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain A: K.74, G.76, E.299 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meyer, T. et al., The plant defense signal galactinol is specifically used as a nutrient by the bacterial pathogenAgrobacterium fabrum. J. Biol. Chem. (2018)

Release Date

2018-04-18

Peptides

Periplasmic alpha-galactoside-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Periplasmic alpha-galactoside-binding protein

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