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

Structure of the PBP MelB (Atu4661) in complex with raffinose from A.fabrum C58

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

1 x FRU- GLC- GLA: alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose(Non-covalent)

FRU-GLC-GLA.1: 17 residues within 4Å: Chain A: W.110, G.111, G.112, I.115, G.192, W.317, R.320, N.333, E.335, N.484, Y.487, S.515, D.519, R.532, R.533, W.639, E.641 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.192, A:R.532, A:R.533, A:R.533, A:W.639, A:G.111, A:G.112, A:R.320, A:R.320, A:N.333, A:E.335, A:Y.487, A:R.533, A:R.533, A:N.484, A:Y.487, A:R.533 Water bridges: A:G.192, A:R.533, A:R.533, A:W.110, A:D.114, A:S.515, A:S.515, A:R.518, A:D.519, A:Y.523, A:Y.523

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

EDO.2: 3 residues within 4Å: Chain A: E.98, N.260 Ligands: CA.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.98 EDO.3: 8 residues within 4Å: Chain A: F.37, P.67, E.68, E.69, K.143, V.159, K.160 Ligands: CA.43 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.68, A:E.69, A:K.160 Water bridges: A:E.69, A:K.143

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

CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.5: 4 residues within 4Å: Chain A: A.182, V.183, D.185, V.188 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:A.182, A:V.183, A:D.185, A:V.188, H2O.5 CA.6: 1 residues within 4Å: Chain A: D.410 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.410, H2O.5, H2O.5, H2O.5, H2O.13 CA.7: 6 residues within 4Å: Chain A: D.458, 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.8: 3 residues within 4Å: Chain A: W.179, T.205, L.206 No protein-ligand interaction detected (PLIP) CA.9: 3 residues within 4Å: Chain A: T.418, A.419, I.420 No protein-ligand interaction detected (PLIP) CA.10: 2 residues within 4Å: Chain A: P.248, S.251 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:P.248, A:S.251, H2O.4 CA.11: 1 residues within 4Å: Chain A: G.76 No protein-ligand interaction detected (PLIP) CA.12: 4 residues within 4Å: Chain A: P.46, W.48, Y.85, N.308 No protein-ligand interaction detected (PLIP) CA.13: 5 residues within 4Å: Chain A: E.265, Y.266, M.267, G.671, E.672 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.672 CA.14: 2 residues within 4Å: Chain A: D.47, W.48 No protein-ligand interaction detected (PLIP) CA.15: 6 residues within 4Å: Chain A: R.96, P.97, Y.280, P.282, D.283, L.314 No protein-ligand interaction detected (PLIP) CA.16: 3 residues within 4Å: Chain A: Y.255, N.256, K.259 No protein-ligand interaction detected (PLIP) CA.17: 3 residues within 4Å: Chain A: S.148, E.149, D.150 No protein-ligand interaction detected (PLIP) CA.18: 4 residues within 4Å: Chain A: T.254, Y.255, N.256 Ligands: CA.22 No protein-ligand interaction detected (PLIP) CA.19: 4 residues within 4Å: Chain A: Q.336, P.337, E.338, T.489 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.489 CA.20: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 3 residues within 4Å: Chain A: P.553, E.566, L.567 No protein-ligand interaction detected (PLIP) CA.22: 3 residues within 4Å: Chain A: T.254, Y.255 Ligands: CA.18 No protein-ligand interaction detected (PLIP) CA.23: 3 residues within 4Å: Chain A: T.254, N.256, Q.257 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.254 CA.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.25: 2 residues within 4Å: Chain A: D.433, R.434 No protein-ligand interaction detected (PLIP) CA.26: 3 residues within 4Å: Chain A: K.574, A.577, R.581 No protein-ligand interaction detected (PLIP) CA.27: 2 residues within 4Å: Chain A: K.414, G.415 No protein-ligand interaction detected (PLIP) CA.28: 1 residues within 4Å: Chain A: L.344 No protein-ligand interaction detected (PLIP) CA.29: 3 residues within 4Å: Chain A: R.391, N.392, E.393 No protein-ligand interaction detected (PLIP) CA.30: 2 residues within 4Å: Chain A: V.82, K.300 No protein-ligand interaction detected (PLIP) CA.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.32: 2 residues within 4Å: Chain A: D.284 Ligands: CA.51 No protein-ligand interaction detected (PLIP) CA.33: 3 residues within 4Å: Chain A: K.623, F.625, S.626 No protein-ligand interaction detected (PLIP) CA.34: 4 residues within 4Å: Chain A: P.15, P.17, A.419, I.420 No protein-ligand interaction detected (PLIP) CA.35: 2 residues within 4Å: Chain A: A.30, R.31 No protein-ligand interaction detected (PLIP) CA.36: 1 residues within 4Å: Chain A: A.30 No protein-ligand interaction detected (PLIP) CA.37: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.38: 4 residues within 4Å: Chain A: N.27, P.79, P.629, Q.630 No protein-ligand interaction detected (PLIP) CA.39: 3 residues within 4Å: Chain A: R.96, S.315, T.316 No protein-ligand interaction detected (PLIP) CA.40: 6 residues within 4Å: Chain A: E.98, Q.106, N.260, F.262, P.263 Ligands: EDO.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.260 CA.41: 5 residues within 4Å: Chain A: D.174, F.177, Y.178, P.237, G.238 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.174, A:G.238 CA.42: 5 residues within 4Å: Chain A: K.133, D.134, F.431, N.589, R.592 No protein-ligand interaction detected (PLIP) CA.43: 4 residues within 4Å: Chain A: E.68, K.160, G.161 Ligands: EDO.3 No protein-ligand interaction detected (PLIP) CA.44: 3 residues within 4Å: Chain A: T.75, G.81, V.82 No protein-ligand interaction detected (PLIP) CA.45: 6 residues within 4Å: Chain A: D.87, T.88, G.657, K.658, Y.659, E.660 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.87, A:T.88 CA.46: 2 residues within 4Å: Chain A: R.90, Y.659 No protein-ligand interaction detected (PLIP) CA.47: 6 residues within 4Å: Chain A: H.91, V.92, G.111, R.320, F.331, E.641 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.111, H2O.6 CA.48: 7 residues within 4Å: Chain A: L.362, I.363, G.364, R.533, N.534, S.539, F.635 No protein-ligand interaction detected (PLIP) CA.49: 4 residues within 4Å: Chain A: P.239, M.269, P.270, V.271 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:P.270, H2O.9, H2O.13 CA.50: 5 residues within 4Å: Chain A: G.455, K.457, N.466, F.467, P.468 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:G.455 CA.51: 4 residues within 4Å: Chain A: R.281, P.282, D.284 Ligands: CA.32 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.282 CA.52: 2 residues within 4Å: Chain A: H.152, K.219 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:K.219

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
A

Periplasmic alpha-galactoside-binding protein

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