SMTL ID : 4b9z.1

Crystal Structure of Agd31B, alpha-transglucosylase, complexed with Acarbose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x GLC- GLC- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC-AC1.1: 17 residues within 4Å: Chain A: Y.179, F.271, D.299, L.300, I.341, Y.376, F.377, W.410, D.412, L.413, E.417, R.463, W.477, D.480, F.513, H.540, Q.542 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.271, A:F.513 Hydrogen bonds: A:D.412, A:D.412, A:E.417, A:R.463, A:R.463, A:D.480, A:H.540, A:H.540, A:Q.542 Water bridges: A:E.343, A:D.480, A:D.480

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

SO4.2: 5 residues within 4Å: Chain A: P.322, T.323, P.324, L.325, D.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.325, A:D.326 SO4.3: 2 residues within 4Å: Chain A: R.58, R.231 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.58, A:R.231 SO4.4: 4 residues within 4Å: Chain A: T.732, D.733, N.734, Q.735 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.732, A:T.732, A:D.733, A:N.734, A:N.734 SO4.5: 5 residues within 4Å: Chain A: E.752, R.753, G.807, R.808, E.809 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.808, A:E.809 Salt bridges: A:R.753, A:R.808 SO4.6: 1 residues within 4Å: Chain A: R.797 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.797

1 x OXL: OXALATE ION(Non-covalent)

OXL.7: 4 residues within 4Å: Chain A: H.731, S.764, R.798, K.817 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.764 Water bridges: A:H.731, A:D.765, A:Y.767, A:R.798 Salt bridges: A:H.731, A:R.798, A:K.817, A:K.817

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

PEG.8: 6 residues within 4Å: Chain A: L.566, R.569, F.640, Y.674, E.690 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.569, A:R.569

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

EDO.9: 2 residues within 4Å: Chain A: W.641 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.569, A:H.660 EDO.10: 2 residues within 4Å: Chain A: E.809, A.810 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.810 EDO.11: 1 residues within 4Å: Chain A: D.683 No protein-ligand interaction detected (PLIP) EDO.12: 5 residues within 4Å: Chain A: H.178, H.184, S.185, G.186 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.184, A:G.186 EDO.13: 5 residues within 4Å: Chain A: R.590, F.594, F.610, G.612, D.613 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.590, A:G.612 EDO.14: 3 residues within 4Å: Chain A: E.276, R.280, T.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.276 Water bridges: A:R.280 EDO.15: 5 residues within 4Å: Chain A: R.176, A.177, H.178, Q.187 Ligands: EDO.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.177 EDO.16: 5 residues within 4Å: Chain A: Q.77, L.78, S.229, G.230, R.231 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.78, A:G.230 Water bridges: A:T.432 EDO.17: 4 residues within 4Å: Chain A: D.783, C.784, A.785, S.786 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.784, A:A.785, A:S.786 Water bridges: A:D.783 EDO.18: 2 residues within 4Å: Chain A: P.562, K.565 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.565 Water bridges: A:R.569 EDO.19: 3 residues within 4Å: Chain A: R.270, E.278, D.543 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.270, A:D.543 EDO.20: 1 residues within 4Å: Chain A: R.176 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.176, A:R.176, A:E.417, A:E.417 EDO.21: 1 residues within 4Å: Chain A: R.255 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.255 EDO.22: 3 residues within 4Å: Chain A: D.596, E.597, K.598 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.597, A:K.598, A:K.598 EDO.23: 1 residues within 4Å: Chain A: R.274 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.274, A:R.274

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsbrink, J. et al., Structural Enzymology of Cellvibrio Japonicus Agd31B Reveals Alpha-Transglucosylase Activity in Glycoside Hydrolase Family 31. J.Biol.Chem. (2012)

Release Date

2012-11-14

Peptides

ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ALPHA-GLUCOSIDASE, PUTATIVE, ADG31B

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