SMTL ID : 5vyz.1

Crystal structure of Lactococcus lactis pyruvate carboxylase in complex with cyclic-di-AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

MN.1: 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.5: 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.8: 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.12: 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

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 22 residues within 4Å: Chain A: K.124, I.139, M.163, K.165, G.169, G.170, G.171, G.172, M.175, E.207, K.208, Y.209, I.210, H.215, Q.239, N.242, E.282, L.284, I.293, E.294, T.450 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.165, A:G.171, A:G.171, A:E.207, A:K.208, A:I.210, A:H.215, A:Q.239, A:N.242, A:T.450 Water bridges: A:Y.209 Salt bridges: A:K.124, A:K.124, A:K.165 ADP.6: 20 residues within 4Å: Chain B: K.124, I.139, M.163, K.165, G.169, G.170, M.175, E.207, K.208, Y.209, I.210, H.215, Q.239, N.242, E.282, L.284, I.293, E.294, T.450 Ligands: MG.7 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.207, B:K.208, B:I.210, B:H.215, B:Q.239, B:N.242, B:T.450, B:T.450 Water bridges: B:Y.209 Salt bridges: B:K.124, B:K.124, B:K.165 ADP.9: 14 residues within 4Å: Chain C: I.139, E.207, K.208, Y.209, I.210, H.215, Q.239, N.242, E.282, L.284, I.293, E.294, T.450 Ligands: MG.10 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:E.207, C:I.210, C:H.215, C:Q.239, C:N.242, C:T.450 ADP.13: 21 residues within 4Å: Chain D: K.124, I.139, M.163, K.165, G.169, G.170, G.172, M.175, E.207, K.208, Y.209, I.210, H.215, Q.239, N.242, E.282, L.284, I.293, E.294, T.450 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:K.165, D:G.169, D:K.208, D:I.210, D:H.215, D:Q.239, D:N.242, D:T.450 Salt bridges: D:K.124, D:K.124, D:K.165

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.282, E.294 Ligands: ADP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.282, A:E.294, H2O.1 MG.7: 3 residues within 4Å: Chain B: E.282, E.294 Ligands: ADP.6 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.282, B:E.294, H2O.13 MG.10: 4 residues within 4Å: Chain C: E.282, E.294, N.296 Ligands: ADP.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.282, C:E.294 MG.14: 3 residues within 4Å: Chain D: E.282, E.294 Ligands: ADP.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.282, D:E.294

2 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.4: 15 residues within 4Å: Chain A: P.719, Q.720, Y.723, I.750, S.753, G.754, Q.757 Chain B: P.719, Q.720, Y.723, R.724, I.750, S.753, G.754, Q.757 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:S.753, B:Q.757, A:S.753, A:S.753, A:Q.757 Water bridges: B:Q.720, B:R.724, B:S.753, B:Q.757, B:A.785, A:A.785 pi-Stacking: B:Y.723, B:Y.723, A:Y.723, A:Y.723 2BA.11: 14 residues within 4Å: Chain C: P.719, Q.720, Y.723, I.750, S.753, G.754, Q.757 Chain D: P.719, Q.720, Y.723, I.750, S.753, G.754, Q.757 14 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:S.753, C:Q.757, D:S.753, D:S.753, D:Q.757 Water bridges: C:Q.720, C:S.753, D:Q.720, D:Q.720, D:R.724, D:A.785 pi-Stacking: C:Y.723, D:Y.723, D:Y.723

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, P.H. et al., Structural and functional studies of pyruvate carboxylase regulation by cyclic di-AMP in lactic acid bacteria. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-08-16

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase