SMTL ID : 7u3b.3 (3 other biounits)

Structure of S. venezuelae GlgX bound to c-di-GMP and acarbose (pH 8.5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-dimer

Ligands

2 x A16: 4-O-(4,6-dideoxy-4-{[(1S,2S,3S,4R,5S)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranosyl)-beta-D-glucopyranose

A16.1: 13 residues within 4Å: Chain A: R.215, W.225, Y.227, G.310, T.311, D.345, E.381, H.452, D.453, E.473, D.477, N.537, Y.539 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.215, A:H.274, A:E.473, A:N.537, A:N.537, A:Y.539 A16.4: 15 residues within 4Å: Chain B: R.215, W.225, Y.227, N.273, H.274, G.310, T.311, D.345, L.346, E.381, H.452, D.453, E.473, N.537, Y.539 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:R.215, B:R.215, B:H.274, B:E.381, B:D.453, B:N.537, B:N.537, B:Y.539

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: P.140, F.142, E.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.142, A:E.336

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: 12 residues within 4Å: Chain A: H.33, R.34, E.50, R.52, E.53, T.54, R.59 Chain B: G.439, R.440, R.441, R.582, F.583 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:R.440, B:R.441, B:R.582, B:F.583, B:S.632, A:R.34, A:R.52, A:T.54, A:T.54, A:R.59, A:R.59 Salt bridges: B:H.585, A:E.50 pi-Cation interactions: A:R.34, A:R.34, A:R.52 C2E.5: 12 residues within 4Å: Chain A: Q.436, R.441, R.582, F.583, H.585 Chain B: H.33, R.34, E.50, R.52, E.53, T.54, R.59 19 PLIP interactions: 6 interactions with chain A, 13 interactions with chain B Hydrogen bonds: A:R.441, A:R.582, A:R.582, A:F.583, A:S.632, B:R.34, B:R.52, B:T.54, B:T.54, B:T.54, B:R.59, B:R.59 Salt bridges: 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
E

B
I

Glycogen debranching enzyme GlgX

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