SMTL ID : 4qsk.1

Crystal Structure of L. monocytogenes Pyruvate Carboxylase in complex with Cyclic-di-AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x 2BA: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide(Non-covalent)

2BA.1: 8 residues within 4Å: Chain A: Q.720, Y.723, Y.750, A.753, A.754, S.757 Chain C: Y.750 Ligands: 2BA.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.723, A:S.757, A:S.757, C:Y.750 pi-Stacking: A:Y.723, A:Y.723 2BA.5: 7 residues within 4Å: Chain B: Y.723, Y.750, A.753, A.754, S.757 Chain D: Y.750 Ligands: 2BA.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.750, B:S.757, B:S.757 pi-Stacking: B:Y.723, B:Y.723 2BA.7: 8 residues within 4Å: Chain A: Y.750 Chain C: Q.720, Y.723, Y.750, A.753, A.754, S.757 Ligands: 2BA.1 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.750, C:S.757, C:S.757 pi-Stacking: C:Y.723, C:Y.723 2BA.11: 7 residues within 4Å: Chain B: Y.750 Chain D: Y.723, Y.750, A.753, A.754, S.757 Ligands: 2BA.5 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:Y.750, D:S.757, D:S.757 pi-Stacking: D:Y.723, D:Y.723

4 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 8 residues within 4Å: Chain A: R.421, R.423, R.466, G.467, L.1047, N.1048, Q.1050, R.1052 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.466, A:G.467, A:N.1048, A:Q.1050 Salt bridges: A:R.421, A:R.421, A:R.423, A:R.423, A:R.1052 FLC.6: 8 residues within 4Å: Chain B: R.421, R.423, R.466, G.467, L.1047, N.1048, Q.1050, R.1052 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.466, B:G.467, B:N.1048, B:Q.1050, B:Q.1050 Salt bridges: B:R.421, B:R.421, B:R.423, B:R.423, B:R.1052 FLC.8: 8 residues within 4Å: Chain C: R.421, R.423, R.466, G.467, L.1047, N.1048, Q.1050, R.1052 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.466, C:G.467, C:N.1048, C:Q.1050 Salt bridges: C:R.421, C:R.421, C:R.423, C:R.423, C:R.1052 FLC.12: 8 residues within 4Å: Chain D: R.421, R.423, R.466, G.467, L.1047, N.1048, Q.1050, R.1052 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.466, D:G.467, D:N.1048, D:Q.1050, D:Q.1050 Salt bridges: D:R.421, D:R.421, D:R.423, D:R.423, D:R.1052

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: D.542, K.711, H.740, H.742 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.542, A:H.740, A:H.742 MN.4: 4 residues within 4Å: Chain B: D.542, K.711, H.740, H.742 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.542, B:H.740, B:H.742 MN.9: 4 residues within 4Å: Chain C: D.542, K.711, H.740, H.742 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.542, C:H.740, C:H.742 MN.10: 4 residues within 4Å: Chain D: D.542, K.711, H.740, H.742 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.542, D:H.740, D:H.742

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sureka, K. et al., The Cyclic Dinucleotide c-di-AMP Is an Allosteric Regulator of Metabolic Enzyme Function. Cell(Cambridge,Mass.) (2014)

Release Date

2014-10-29

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate carboxylase