SMTL ID : 6m5a.1

Crystal structure of GH121 beta-L-arabinobiosidase HypBA2 from Bifidobacterium longum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

PEG.1: 5 residues within 4Å: Chain A: I.54, D.55, T.56, A.292, Y.295 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.56, A:T.56 Water bridges: A:N.184, A:N.184 PEG.4: 6 residues within 4Å: Chain A: Y.105, L.355, G.356, Y.357, W.721, I.722 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.105 Water bridges: A:Y.94 PEG.6: 6 residues within 4Å: Chain A: A.517, Q.518, K.521, A.529, E.530, Q.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.518, A:K.521 Water bridges: A:Q.533 PEG.8: 7 residues within 4Å: Chain A: Q.540, G.580, L.581, M.582, P.583, T.584 Ligands: PEG.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.540, A:Q.540, A:T.584 Water bridges: A:Q.533, A:T.584 PEG.11: 7 residues within 4Å: Chain A: Y.577, S.578, G.580, T.584, N.644, Y.645 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.578, A:Y.645 PEG.13: 5 residues within 4Å: Chain A: N.625, S.627, N.630, F.683, L.727 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.625, A:N.630 PEG.18: 6 residues within 4Å: Chain A: D.192, R.193, D.194, S.253, L.254, K.255 No protein-ligand interaction detected (PLIP) PEG.19: 5 residues within 4Å: Chain A: L.453, A.454, D.469, N.470, S.471 No protein-ligand interaction detected (PLIP)

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 8 residues within 4Å: Chain A: R.98, G.99, R.100, Y.177, Y.302, R.332, F.333, M.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.305, A:R.332 Water bridges: A:Y.380, A:Y.380 PGE.7: 7 residues within 4Å: Chain A: Y.399, A.446, E.447, Q.450, Y.520, N.528, K.531 No protein-ligand interaction detected (PLIP) PGE.15: 4 residues within 4Å: Chain A: K.394, S.395, K.396, G.398 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.394, A:K.394, A:K.396, A:G.398 Water bridges: A:K.394, A:K.396 PGE.23: 6 residues within 4Å: Chain A: D.687, N.688, I.700, N.701, N.702, K.705 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.705 Water bridges: A:N.702, A:N.702

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

EDO.3: 4 residues within 4Å: Chain A: Q.41, F.44, K.304, V.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.41, A:K.304 EDO.9: 4 residues within 4Å: Chain A: W.548, N.586, D.588, Y.589 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.548, A:N.586 EDO.10: 3 residues within 4Å: Chain A: L.560, N.561, G.563 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.561 EDO.12: 3 residues within 4Å: Chain A: R.594, E.597, D.598 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: A.789, T.802, D.804, Q.827, V.828, T.829 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.829, A:T.829 EDO.16: 3 residues within 4Å: Chain A: G.816, T.817, V.818 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.818 EDO.17: 3 residues within 4Å: Chain A: K.836, N.837, V.838 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.837, A:V.838 EDO.20: 4 residues within 4Å: Chain A: S.89, D.90, N.93, Y.94 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.93, A:Y.94 Water bridges: A:S.89 EDO.21: 5 residues within 4Å: Chain A: A.13, Y.14, D.80, N.712, G.713 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.712, A:G.713 Water bridges: A:Y.14 EDO.22: 3 residues within 4Å: Chain A: Y.228, N.271, T.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.277, A:T.277

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

PG4.5: 6 residues within 4Å: Chain A: G.494, R.495, S.496, Q.498, N.561, D.562 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.496, A:Q.498, A:N.561 Water bridges: A:P.493, A:R.495, A:S.496, A:D.562

3 x CA: CALCIUM ION(Non-covalent)

CA.24: 6 residues within 4Å: Chain A: N.466, N.468, N.470, L.472, D.474, D.501 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.472, A:D.474, A:D.501 CA.25: 5 residues within 4Å: Chain A: D.693, N.695, D.697, V.699, D.704 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.693, A:D.697, A:V.699, A:D.704, H2O.3 CA.26: 4 residues within 4Å: Chain A: D.314, T.315, D.318, D.321 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.314, A:T.315, A:D.318, A:D.321, H2O.8, H2O.16

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saito, K. et al., Crystal structure of beta-L-arabinobiosidase belonging to glycoside hydrolase family 121. Plos One (2020)

Release Date

2020-06-03

Peptides

Beta-L-arabinobiosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-L-arabinobiosidase