SMTL ID : 7u3d.1 (1 other biounit)

Structure of S. venezuelae GlgX-c-di-GMP-acarbose complex (4.6)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 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

GLC-GLC-AC1.1: 15 residues within 4Å: Chain B: R.215, W.225, Y.227, H.274, D.307, G.310, T.311, R.343, D.345, H.452, D.453, E.473, D.477, N.537, Y.539 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.215, B:N.279, B:D.307, B:E.473, B:Y.539, B:D.453, B:N.537, B:N.537 Water bridges: B:N.223, B:Y.227, B:Y.227, B:Y.227, B:Y.227, B:N.228, B:D.453 GLC-GLC-AC1.2: 15 residues within 4Å: Chain A: N.223, W.225, Y.227, H.274, N.279, G.310, T.311, R.343, D.345, E.381, H.452, D.453, E.473, N.537, Y.539 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.215, A:E.473, A:Y.539, A:N.223, A:D.453, A:N.537, A:N.537 Water bridges: A:N.537, A:Y.227, A:Y.227, A:Y.227, A:G.478

2 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.3: 15 residues within 4Å: Chain A: H.33, R.34, E.50, R.52, E.53, T.54, R.59 Chain B: Q.436, G.439, R.440, R.441, R.582, F.583, H.585, S.632 26 PLIP interactions: 15 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:R.34, A:R.52, A:R.52, A:T.54, A:T.54, A:R.59, B:Q.436, B:R.440, B:R.441, B:R.441, B:R.582, B:F.583, B:S.632, B:S.632 Water bridges: A:R.34, A:E.50, A:D.55, B:R.582, B:H.585 Salt bridges: A:E.50, A:R.52, A:D.55, B:H.585 pi-Cation interactions: A:R.34, A:R.34, A:R.52 C2E.4: 15 residues within 4Å: Chain A: Q.436, G.439, R.440, R.441, R.582, F.583, H.585, S.632 Chain B: H.33, R.34, E.50, R.52, E.53, T.54, R.59 26 PLIP interactions: 13 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:Q.436, A:R.440, A:R.441, A:R.441, A:F.583, A:S.632, B:R.34, B:R.52, B:R.52, B:T.54, B:T.54, B:R.59 Water bridges: A:R.441, A:R.582, A:R.582, A:H.585, A:H.585, B:E.50 Salt bridges: A:R.582, A:H.585, B:E.50, B:R.52 pi-Cation interactions: B:R.34, B:R.34, B:R.52, B:R.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schumacher, M.A. et al., Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP. Nat Commun (2022)

Release Date

2022-10-05

Peptides

Glycogen debranching enzyme GlgX: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

Glycogen debranching enzyme GlgX

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