SMTL ID : 6eq0.2 (1 other biounit)

Structure of the periplasmic binding protein (PBP) MelB (atu4661) in complex with galactose from agrobacterium tumefacien C58

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

1 x GLA: alpha-D-galactopyranose(Non-covalent)

GLA.1: 12 residues within 4Å: Chain A: W.110, G.111, G.112, W.317, R.320, N.333, E.335, Y.487, R.533, W.639, E.641 Ligands: CA.23 12 PLIP interactions: 12 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:Y.487, A:Y.487, A:Y.487, A:R.533, A:R.533 Salt bridges: A:R.533

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

EDO.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.4: 2 residues within 4Å: Chain A: P.416, F.417 No protein-ligand interaction detected (PLIP) EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.6: 3 residues within 4Å: Chain A: E.388, R.391, N.392 No protein-ligand interaction detected (PLIP) EDO.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: S.430, F.431, A.593 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.430 EDO.10: 2 residues within 4Å: Chain A: P.350, K.623 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.623 EDO.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.12: 2 residues within 4Å: Chain A: T.429, S.430 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: Q.630 Ligand excluded by PLIP CL.14: 1 residues within 4Å: Chain A: N.27 Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: G.95, R.96, D.514, N.516 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain A: K.252 Ligand excluded by PLIP

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.19: 7 residues within 4Å: Chain A: D.458, T.459, D.460, D.462, F.464, N.466, N.476 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.458, A:D.460, A:D.462, A:F.464 CA.20: 2 residues within 4Å: Chain A: E.265, M.267 No protein-ligand interaction detected (PLIP) CA.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.22: 4 residues within 4Å: Chain A: E.537, Q.547, Y.603, Y.608 No protein-ligand interaction detected (PLIP) CA.23: 2 residues within 4Å: Chain A: Y.487 Ligands: GLA.1 No protein-ligand interaction detected (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

2018-04-11

Peptides

Periplasmic alpha-galactoside-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Periplasmic alpha-galactoside-binding protein

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