SMTL ID : 7ehh.1

Crystal structure of alpha-glucosidase from Weissella cibaria BKK1 in complex with maltose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 14 residues within 4Å: Chain A: H.214, Y.216, H.256, E.296, F.306, M.312, R.343, N.345, V.346, E.374, H.439, D.440, D.484, R.488 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.484, A:R.488, A:R.488 Water bridges: A:H.214, A:E.296, A:E.296, A:T.309 GLC-GLC.14: 14 residues within 4Å: Chain B: H.214, Y.216, H.256, E.296, F.306, M.312, R.343, N.345, V.346, E.374, H.439, D.440, D.484, R.488 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.484, B:R.488, B:R.488 Water bridges: B:H.214, B:E.296, B:T.309

4 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 8 residues within 4Å: Chain A: W.168, D.169, S.170, M.491, V.492, W.493, Q.494, L.497 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.170, A:S.170, A:S.170, A:W.493, A:Q.494 Salt bridges: A:D.169 MES.3: 2 residues within 4Å: Chain A: H.449, E.450 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.449, A:E.450 MES.15: 8 residues within 4Å: Chain B: W.168, D.169, S.170, M.491, V.492, W.493, Q.494, L.497 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.170, B:S.170, B:S.170, B:W.493, B:Q.494 Salt bridges: B:D.169 MES.16: 2 residues within 4Å: Chain B: H.449, E.450 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: K.166, D.172, H.173 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.166, A:K.166, A:D.172, A:D.172, A:H.173 GOL.12: 2 residues within 4Å: Chain A: G.175, R.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.176 Water bridges: A:E.177, A:E.177 GOL.13: 11 residues within 4Å: Chain A: I.375, W.376, H.377, M.392, N.393, Y.394, S.395, Y.396, Q.420, Y.424, M.432 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:I.375, A:N.393, A:Y.394, A:S.395, A:Y.396, A:Q.420, A:Y.424 Water bridges: A:N.393 GOL.17: 3 residues within 4Å: Chain B: K.166, D.172, H.173 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.166, B:K.166, B:D.172, B:H.173 GOL.25: 2 residues within 4Å: Chain B: G.175, R.176 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.176 Water bridges: B:E.177, B:E.177 GOL.26: 11 residues within 4Å: Chain B: I.375, W.376, H.377, M.392, N.393, Y.394, S.395, Y.396, Q.420, Y.424, M.432 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:I.375, B:N.393, B:Y.394, B:S.395, B:Y.396, B:Q.420, B:Y.424, B:Y.424 Water bridges: B:N.393

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: N.155, D.157, N.160, D.161, G.181, D.183 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.157, A:D.161, A:G.181, A:D.183, H2O.6 CA.18: 6 residues within 4Å: Chain B: N.155, D.157, N.160, D.161, G.181, D.183 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.157, B:D.161, B:G.181, B:D.183, H2O.23

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 2 residues within 4Å: Chain A: D.230, A.231 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.231 Water bridges: A:D.230 SO4.7: 7 residues within 4Å: Chain A: M.8, R.10, R.29 Chain B: M.8, R.10, R.29 Ligands: SO4.20 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Water bridges: A:R.10, B:R.10, B:R.10 Salt bridges: A:R.10, A:R.29, B:R.10, B:R.29 SO4.8: 5 residues within 4Å: Chain A: D.189, H.190, D.192, H.193, W.493 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.192, A:H.193 Water bridges: A:D.189 Salt bridges: A:H.190 SO4.9: 3 residues within 4Å: Chain A: P.162, V.163, H.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.163 Salt bridges: A:H.227 SO4.10: 2 residues within 4Å: Chain A: T.292, D.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.291, A:D.293 SO4.11: 2 residues within 4Å: Chain A: T.555, D.556 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.556 SO4.19: 2 residues within 4Å: Chain B: D.230, A.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.231 SO4.20: 7 residues within 4Å: Chain A: M.8, R.10, R.29 Chain B: M.8, R.10, R.29 Ligands: SO4.7 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Water bridges: A:R.10, A:R.10, A:R.29, B:R.10 Salt bridges: A:R.10, A:R.29, B:R.10, B:R.29 SO4.21: 5 residues within 4Å: Chain B: D.189, H.190, D.192, H.193, W.493 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.192, B:H.193 Water bridges: B:D.189 Salt bridges: B:H.190 SO4.22: 3 residues within 4Å: Chain B: P.162, V.163, H.227 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.163 Salt bridges: B:H.227 SO4.23: 2 residues within 4Å: Chain B: T.292, D.293 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.291, B:D.293 SO4.24: 2 residues within 4Å: Chain B: T.555, D.556 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.556

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wangpaiboon, K. et al., A GH13 alpha-glucosidase from Weissella cibaria uncommonly acts on short-chain maltooligosaccharides. Acta Crystallogr D Struct Biol (2021)

Release Date

2021-08-11

Peptides

alpha-glucosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

alpha-glucosidase

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