SMTL ID : 7u3a.2 (1 other biounit)

Structure of the Streptomyces venezuelae GlgX-c-di-GMP complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.34 Å

Oligo State

homo-dimer

Ligands

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)(Covalent)

C2E.1: 16 residues within 4Å: Chain A: H.33, R.34, E.50, R.52, E.53, T.54, D.55, A.56, R.59 Chain B: Q.436, G.439, R.440, R.441, R.582, F.583, S.632 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:R.34, A:R.52, A:R.52, A:T.54, A:T.54, A:A.56, A:R.59, A:R.59, B:Q.436, B:G.439, B:F.583, B:S.632 Salt bridges: A:E.50, A:R.52, B:H.585 pi-Cation interactions: A:R.34, A:R.52 C2E.2: 16 residues within 4Å: Chain A: Q.436, G.439, R.440, R.441, R.582, F.583, S.632 Chain B: H.33, R.34, E.50, R.52, E.53, T.54, D.55, A.56, R.59 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:R.34, B:R.52, B:R.52, B:T.54, B:T.54, B:A.56, B:R.59, A:Q.436, A:G.439, A:R.441, A:R.582, A:F.583, A:S.632, A:S.632 Salt bridges: B:E.50, B:R.52, A:R.582 pi-Cation interactions: B:R.34, B:R.34, 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
C

B
D

Glycogen debranching enzyme GlgX

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