SMTL ID : 5l6v.1 (3 other biounits)

Crystal structure of E. coli ADP-glucose pyrophosphorylase (AGPase) in complex with a negative allosteric regulator adenosine monophosphate (AMP) - AGPase*AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

homo-tetramer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 13 residues within 4Å: Chain A: T.117, A.140, D.142, H.143, A.177, F.178, G.179, E.194, K.195, S.212, M.213, G.214, Y.216 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.142, A:K.195, A:K.195, A:H.143, A:G.179, A:E.194, A:S.212, A:D.239 Water bridges: A:S.212

4 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 10 residues within 4Å: Chain A: K.39, R.40, H.46, R.52, T.79, E.370, R.386, A.387, R.419 Chain C: R.130 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:K.39, A:E.370, C:R.130, C:R.130 Salt bridges: A:R.40, A:H.46, A:R.52, A:R.386 pi-Cation interactions: C:R.130 AMP.3: 11 residues within 4Å: Chain B: K.39, R.40, H.46, R.52, T.79, E.370, R.386, A.387, R.419 Chain D: I.127, R.130 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:K.39, B:T.79, B:E.370, D:R.130, D:R.130 Water bridges: B:K.39 Salt bridges: B:R.40, B:H.46, B:R.52, B:R.386 pi-Cation interactions: D:R.130 AMP.4: 11 residues within 4Å: Chain A: I.127, R.130 Chain C: K.39, R.40, H.46, R.52, T.79, E.370, R.386, A.387, R.419 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:K.39, C:T.79, C:E.370, A:R.130, A:R.130 Water bridges: C:Q.82, C:R.419 Salt bridges: C:R.40, C:H.46, C:R.52, C:R.386 pi-Cation interactions: A:R.130 AMP.5: 10 residues within 4Å: Chain B: R.130 Chain D: K.39, R.40, H.46, R.52, T.79, E.370, R.386, A.387, R.419 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:R.130, D:K.39, D:E.370 pi-Cation interactions: B:R.130 Salt bridges: D:R.40, D:H.46, D:R.52, D:R.386

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

PO4.6: 3 residues within 4Å: Chain D: G.30, T.31, R.32 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.30, D:T.31, D:T.31, D:R.32, D:G.278 Salt bridges: D:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cifuente, J.O. et al., Structural Basis of Glycogen Biosynthesis Regulation in Bacteria. Structure (2016)

Release Date

2016-09-07

Peptides

Glucose-1-phosphate adenylyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Glucose-1-phosphate adenylyltransferase

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