- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 1 x BTN: BIOTIN(Covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
MN.3: 5 residues within 4Å:- Chain A: D.540, K.709, H.738, H.740, Q.774
3 PLIP interactions:3 interactions with chain A- Metal complexes: A:D.540, A:H.738, A:H.740
MN.10: 6 residues within 4Å:- Chain B: R.539, D.540, K.709, H.738, H.740, Q.774
3 PLIP interactions:3 interactions with chain B- Metal complexes: B:D.540, B:H.738, B:H.740
MN.16: 4 residues within 4Å:- Chain C: D.540, K.709, H.738, H.740
4 PLIP interactions:3 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.540, C:H.738, C:H.740, H2O.5
MN.22: 5 residues within 4Å:- Chain D: D.540, K.709, H.738, H.740, Q.774
3 PLIP interactions:3 interactions with chain D- Metal complexes: D:D.540, D:H.738, D:H.740
- 1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
ATP.4: 24 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, H.213, Q.237, N.240, E.280, L.282, I.291, E.292, N.294, R.296, T.448
- Ligands: MG.5
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:G.167, A:G.169, A:G.170, A:K.206, A:I.208, A:H.213, A:H.213, A:Q.237, A:E.292, A:N.294, A:R.296, A:T.448
- Water bridges: A:E.93, A:G.167
- Salt bridges: A:K.122, A:K.122, A:K.122, A:K.163
- 4 x ACO: ACETYL COENZYME *A(Non-covalent)
ACO.6: 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, I.1017, G.1020, K.1021, T.1022, L.1023, N.1046, R.1050
- Chain C: F.23, R.24, N.27, R.47, F.48, K.49, A.50, D.51, S.53
19 PLIP interactions:16 interactions with chain A, 3 interactions with chain C- Hydrophobic interactions: A:E.419, C:K.49
- Hydrogen bonds: A:R.368, A:R.421, A:R.421, A:R.464, A:D.465, A:R.466, A:K.1021, A:K.1021, A:T.1022, A:N.1046, C:A.50, C:S.53
- Salt bridges: A:R.368, A:R.423, A:R.423, A:R.466, A:R.1050
ACO.13: 28 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, E.52, S.53
26 PLIP interactions:20 interactions with chain B, 6 interactions with chain D- Hydrogen bonds: B:R.368, B:H.418, B:R.421, B:R.421, B:R.464, B:R.464, B:R.466, B:K.1021, B:T.1022, B:N.1046, D:A.50, D:S.53
- Water bridges: B:R.368, B:R.368, B:K.1021, D:A.50
- Salt bridges: B:R.368, B:R.423, B:R.423, B:R.466, B:K.1021, B:R.1050
- pi-Cation interactions: B:K.1021
- 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
21 PLIP interactions:16 interactions with chain C, 5 interactions with chain A- Hydrogen bonds: C:R.368, C:R.421, C:R.421, C:R.464, C:D.465, C:R.466, C:K.1021, C:T.1022, C:N.1046, A:A.50, A:S.53
- Water bridges: C:G.467
- Salt bridges: C:R.368, C:R.421, 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: 28 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, D.465, R.466, G.467, I.1017, G.1020, K.1021, T.1022, L.1023, N.1046, R.1050
20 PLIP interactions:14 interactions with chain D, 6 interactions with chain B- Hydrogen bonds: D:R.368, D:R.421, D:R.421, D:R.464, D:D.465, D:R.466, D:G.467, D:T.1022, D:N.1046, B:N.27, B:A.50, B:S.53
- Salt bridges: D:R.368, D:R.423, D:R.423, D:R.466, D:R.1050
- Hydrophobic interactions: B:F.23, B:R.24, B:K.49
- 4 x PYR: PYRUVIC ACID(Non-covalent)
PYR.7: 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
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:V.872
- Hydrogen bonds: A:R.539, A:R.539, A:Q.543, A:A.578, A:T.873
- Salt bridges: A:R.539, A:R.612
PYR.14: 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
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:L.610, B:F.645, B:V.872
- Hydrogen bonds: B:R.539, B:R.539, B:Q.543, B:A.578
- 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
9 PLIP interactions:9 interactions with chain C- Hydrophobic interactions: C:L.610, C:F.645, C:V.872
- Hydrogen bonds: C:R.539, C:Q.543, C:Q.543, C:A.578
- Salt bridges: C:R.539, C:R.612
PYR.26: 10 residues within 4Å:- Chain D: R.539, Q.543, G.577, A.578, L.610, R.612, F.645, K.709, V.872, T.873
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:V.872
- Hydrogen bonds: D:R.539, D:Q.543, D:Q.543, D:A.578
- Salt bridges: D:R.612
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.11: 21 residues within 4Å:- Chain B: K.122, M.161, K.163, G.167, G.168, G.169, 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.12
9 PLIP interactions:9 interactions with chain B- Hydrogen bonds: B:G.167, B:G.169, B:K.206, B:I.208, B:H.213, B:Q.237
- Salt bridges: B:K.122, B:K.122, B:K.163
ADP.17: 21 residues within 4Å:- Chain C: K.122, I.137, M.161, K.163, G.168, G.169, G.170, M.173, E.205, K.206, Y.207, I.208, 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.169, C:G.170, C:E.205, 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: 21 residues within 4Å:- Chain D: K.122, I.137, M.161, K.163, G.168, G.169, G.170, M.173, E.205, 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:K.163, D:G.169, D:G.170, D:E.205, D:E.205, D:I.208, D:H.213, D:Q.237
- Salt bridges: D:K.122, D:K.122, D:K.163
- 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
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY
- Oligo State
- homo-tetramer
- Ligands
- 1 x BTN: BIOTIN(Covalent)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 4 x ACO: ACETYL COENZYME *A(Non-covalent)
- 4 x PYR: PYRUVIC ACID(Non-covalent)
- 1 x BCT: BICARBONATE ION(Non-functional Binders)
- 3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 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
AB
BC
CD
D