SMTL ID : 7zz8.1

Cryo-EM structure of Lactococcus lactis pyruvate carboxylase with acetyl-CoA and cyclic di-AMP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: V.525, T.528, D.759, R.789 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:V.525, A:T.528, A:D.759 MG.4: 3 residues within 4Å: Chain A: E.280, E.292 Ligands: ADP.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.280, A:E.280, A:E.292 MG.8: 5 residues within 4Å: Chain B: V.525, K.526, T.528, D.759, R.789 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:V.525, B:T.528, B:D.759 MG.11: 4 residues within 4Å: Chain B: H.213, E.280, E.292 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.280, B:E.280 MG.15: 3 residues within 4Å: Chain C: V.525, T.528, R.789 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:V.525, C:T.528 MG.18: 3 residues within 4Å: Chain C: E.280, E.292 Ligands: ADP.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.280, C:E.280, C:E.292 MG.21: 4 residues within 4Å: Chain D: V.525, T.528, D.759, R.789 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:V.525, D:T.528, D:D.759 MG.24: 3 residues within 4Å: Chain D: E.280, E.292 Ligands: ADP.23 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.280, D:E.280, D:E.292

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

MN.2: 5 residues within 4Å: Chain A: D.540, K.709, H.738, H.740, Q.774 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.540, A:H.738, A:H.740, H2O.1 MN.9: 5 residues within 4Å: Chain B: D.540, K.709, H.738, H.740, Q.774 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.540, B:H.738, B:H.740, H2O.1 MN.16: 5 residues within 4Å: Chain C: D.540, K.709, H.738, H.740, Q.774 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.738, C:H.740, H2O.1 MN.22: 6 residues within 4Å: Chain D: R.539, D.540, K.709, H.738, H.740, Q.774 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.540, D:H.738, D:H.740, H2O.1

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

ADP.3: 23 residues within 4Å: Chain A: K.122, I.137, M.161, K.163, G.167, G.168, G.169, G.170, M.173, E.205, K.206, Y.207, I.208, P.211, H.213, Q.237, N.240, E.280, L.282, I.291, E.292, T.448 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.167, A:G.169, A:G.170, A:E.205, A:I.208, A:Q.237, A:T.448 Salt bridges: A:K.122, A:K.122, A:K.163 ADP.10: 19 residues within 4Å: Chain B: K.122, M.161, K.163, G.167, G.168, G.169, G.170, M.173, E.205, K.206, Y.207, I.208, H.213, Q.237, N.240, L.282, E.292, T.448 Ligands: MG.11 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:K.163, B:G.169, B:G.170, B:E.205, B:I.208, B:Q.237, B:E.292, B:E.292, B:T.448 Salt bridges: B:K.122, B:K.122 ADP.17: 22 residues within 4Å: Chain C: K.122, M.161, K.163, G.167, G.168, G.169, G.170, M.173, E.205, K.206, Y.207, I.208, P.211, H.213, Q.237, N.240, E.280, L.282, I.291, E.292, T.448 Ligands: MG.18 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:K.163, C:G.167, C:G.169, C:G.170, C:K.206, C:I.208, C:H.213, C:Q.237, C:T.448 Salt bridges: C:K.122, C:K.122, C:K.163 ADP.23: 20 residues within 4Å: Chain D: K.122, I.137, M.161, K.163, G.168, G.169, G.170, M.173, K.206, Y.207, I.208, H.213, Q.237, N.240, E.280, L.282, I.291, E.292, T.448 Ligands: MG.24 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.167, D:G.169, D:G.170, D:K.206, D:I.208, D:Q.237, D:E.292, D:T.448 Salt bridges: D:K.122, D:K.122, D:K.163

4 x ACO: ACETYL COENZYME *A(Non-covalent)

ACO.5: 27 residues within 4Å: Chain A: R.368, R.415, H.418, E.419, R.421, R.423, L.463, R.464, D.465, R.466, G.467, G.1020, K.1021, T.1022, L.1023, L.1045, N.1046, R.1050 Chain C: F.23, R.24, N.27, R.47, F.48, K.49, A.50, D.51, S.53 18 PLIP interactions: 4 interactions with chain C, 14 interactions with chain A Hydrophobic interactions: C:F.23, C:K.49 Hydrogen bonds: C:N.27, C:A.50, A:R.368, A:R.421, A:R.421, A:R.464, A:D.465, A:R.466, A:G.467, A:T.1022, A:N.1046 Salt bridges: A:R.368, A:R.423, A:R.423, A:R.466, A:R.1050 ACO.12: 27 residues within 4Å: Chain B: R.368, R.415, H.418, E.419, R.421, R.423, L.463, R.464, D.465, R.466, G.467, I.1017, G.1020, K.1021, T.1022, L.1023, N.1046, R.1050 Chain D: F.23, R.24, N.27, R.47, F.48, K.49, A.50, D.51, S.53 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:R.368, B:R.421, B:R.421, B:R.464, B:D.465, B:D.465, B:R.466, B:K.1021, B:T.1022, B:N.1046, D:A.50 Salt bridges: B:R.368, B:R.421, B:R.423, B:R.423, B:R.466, B:R.1050 Hydrophobic interactions: D:F.23, D:R.24, D:K.49 ACO.19: 28 residues within 4Å: Chain A: F.23, R.24, N.27, R.47, F.48, K.49, A.50, D.51, E.52, S.53 Chain C: R.368, R.415, H.418, E.419, R.421, R.423, L.463, R.464, D.465, R.466, G.467, I.1017, G.1020, K.1021, T.1022, L.1023, N.1046, R.1050 19 PLIP interactions: 14 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:R.368, C:R.421, C:R.421, C:R.464, C:R.466, C:G.467, C:K.1021, C:T.1022, C:N.1046, A:A.50, A:S.53 Salt bridges: C:R.368, C:R.423, C:R.423, C:R.466, C:R.1050 Hydrophobic interactions: A:F.23, A:R.24, A:K.49 ACO.25: 26 residues within 4Å: Chain B: F.23, R.24, N.27, R.47, F.48, K.49, A.50, D.51, E.52, S.53 Chain D: R.368, R.415, H.418, E.419, R.421, R.423, L.463, R.464, R.466, I.1017, G.1020, K.1021, T.1022, L.1023, N.1046, R.1050 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain B Hydrogen bonds: D:R.368, D:H.418, D:R.421, D:R.421, D:R.464, D:R.464, D:R.466, D:T.1022, D:N.1046, B:A.50 Salt bridges: D:R.368, D:R.421, D:R.423, D:R.423, D:R.466, D:R.1050 Hydrophobic interactions: B:K.49

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.6: 10 residues within 4Å: Chain A: R.539, Q.543, G.577, A.578, L.610, R.612, F.645, K.709, V.872, T.873 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.610, A:V.872 Hydrogen bonds: A:R.539, A:Q.543, A:A.578, A:T.873 Salt bridges: A:R.612 PYR.13: 10 residues within 4Å: Chain B: R.539, Q.543, G.577, A.578, L.610, R.612, F.645, K.709, V.872, T.873 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.872 Hydrogen bonds: B:R.539, B:Q.543, B:A.578, B:T.873 Salt bridges: B:R.539, B:R.612 PYR.20: 10 residues within 4Å: Chain C: R.539, Q.543, G.577, A.578, L.610, R.612, F.645, K.709, V.872, T.873 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.872 Hydrogen bonds: C:Q.543, C:Q.543, C:A.578 Water bridges: C:R.539 Salt bridges: C:R.539, C:R.612 PYR.26: 9 residues within 4Å: Chain D: R.539, Q.543, G.577, L.610, R.612, F.645, K.709, V.872, T.873 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.872, D:T.873 Hydrogen bonds: D:Q.543 Salt bridges: D:R.539, D:R.612

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.7: 12 residues within 4Å: Chain A: Q.718, Y.721, I.748, S.751, G.752, Q.755 Chain D: Q.718, Y.721, I.748, S.751, G.752, Q.755 11 PLIP interactions: 6 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:Q.718, D:Y.721, D:S.751, D:Q.755, A:Y.721, A:S.751, A:Q.755 pi-Stacking: D:Y.721, D:Y.721, A:Y.721, A:Y.721 2BA.14: 12 residues within 4Å: Chain B: Q.718, Y.721, I.748, S.751, G.752, Q.755 Chain C: Q.718, Y.721, I.748, S.751, G.752, Q.755 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:Y.721, B:S.751, B:S.751, B:Q.755, C:Y.721, C:S.751, C:Q.755 pi-Stacking: B:Y.721, B:Y.721, C:Y.721, C:Y.721

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Alonso, J.P. et al., CryoEM structural exploration of catalytically active enzyme pyruvate carboxylase. Nat Commun (2022)

Release Date

2022-10-12

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase

Related Entries With Identical Sequence