SMTL ID : 3tw6.2 (1 other biounit)

Structure of Rhizobium etli pyruvate carboxylase T882A with the allosteric activator, acetyl coenzyme-A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: Y.639, Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain D: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.22: 5 residues within 4Å: Chain D: Y.639, Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP

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

ADP.3: 16 residues within 4Å: Chain A: M.175, K.177, M.187, E.219, K.220, L.221, V.222, H.227, Q.251, N.254, E.294, I.307, E.308, T.465 Ligands: MG.5, PAE.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.220, A:H.227, A:Q.251, A:E.308 Salt bridges: A:K.177 ADP.10: 14 residues within 4Å: Chain B: K.177, M.187, E.219, K.220, L.221, V.222, H.227, Q.251, N.254, E.294, L.296, E.308, T.465 Ligands: MG.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.220, B:V.222, B:H.227, B:Q.251, B:N.254 Salt bridges: B:K.177 ADP.16: 16 residues within 4Å: Chain C: M.175, K.177, M.187, E.219, K.220, L.221, V.222, H.227, Q.251, N.254, E.294, I.307, E.308, T.465 Ligands: MG.18, PAE.19 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:E.219, C:K.220, C:V.222, C:H.227, C:Q.251, C:E.308, C:E.308, C:T.465 Salt bridges: C:K.177 ADP.23: 14 residues within 4Å: Chain D: K.177, M.187, E.219, K.220, L.221, V.222, H.227, Q.251, N.254, E.294, L.296, E.308, T.465 Ligands: MG.25 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.220, D:V.222, D:Q.251, D:N.254, D:E.308, D:T.465 Salt bridges: D:K.177

4 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: D.560, K.729, H.758, H.760, Q.794 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.560, A:H.758, A:H.760, H2O.6 ZN.11: 5 residues within 4Å: Chain B: D.560, K.729, H.758, H.760, Q.794 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.560, B:H.758, B:H.760, H2O.343 ZN.17: 5 residues within 4Å: Chain C: D.560, K.729, H.758, H.760, Q.794 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.560, C:H.758, C:H.760, H2O.362 ZN.24: 5 residues within 4Å: Chain D: D.560, K.729, H.758, H.760, Q.794 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.560, D:H.758, D:H.760, H2O.699

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: E.294, E.308 Ligands: ADP.3, PAE.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.294, A:E.308, H2O.148 MG.12: 4 residues within 4Å: Chain B: E.294, E.308, N.310 Ligands: ADP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.294, B:E.308 MG.13: 4 residues within 4Å: Chain B: M.545, R.546, E.548, D.779 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.545, B:E.548, B:D.779, H2O.159, H2O.356 MG.18: 4 residues within 4Å: Chain C: E.294, E.308 Ligands: ADP.16, PAE.19 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.294, C:E.308, H2O.504 MG.25: 4 residues within 4Å: Chain D: E.294, E.308, N.310 Ligands: ADP.23 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.294, D:E.308 MG.26: 4 residues within 4Å: Chain D: M.545, R.546, E.548, D.779 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:M.545, D:E.548, D:D.779, H2O.515, H2O.712

2 x PAE: PHOSPHONOACETIC ACID(Non-covalent)

PAE.6: 9 residues within 4Å: Chain A: K.256, E.294, N.310, R.312, Q.314, V.315, E.316 Ligands: ADP.3, MG.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.310, A:R.312, A:R.312, A:Q.314, A:V.315, A:E.316 Water bridges: A:K.256 Salt bridges: A:K.256, A:R.312 PAE.19: 9 residues within 4Å: Chain C: K.256, E.294, N.310, R.312, Q.314, V.315, E.316 Ligands: ADP.16, MG.18 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:N.310, C:R.312, C:R.312, C:Q.314, C:V.315, C:E.316 Water bridges: C:K.256 Salt bridges: C:K.256, C:R.312

2 x COA: COENZYME A(Non-covalent)

COA.7: 15 residues within 4Å: Chain A: R.438, R.440, K.479, R.480, Q.481, D.482, R.483, A.484, I.1037, T.1042, L.1043, L.1065, N.1066 Chain D: R.54, F.55 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:Q.481, A:D.482, A:R.483, A:A.484, A:N.1066, D:R.54, D:A.57 Salt bridges: A:R.438, A:R.440, A:R.483 COA.20: 15 residues within 4Å: Chain B: R.54, F.55 Chain C: R.438, R.440, K.479, R.480, Q.481, D.482, R.483, A.484, I.1037, T.1042, L.1043, L.1065, N.1066 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:R.54, B:A.57, C:Q.481, C:D.482, C:R.483, C:A.484, C:N.1066 Salt bridges: C:R.438, C:R.440, C:R.483

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lietzan, A.D. et al., Interaction between the biotin carboxyl carrier domain and the biotin carboxylase domain in pyruvate carboxylase from Rhizobium etli. Biochemistry (2011)

Release Date

2011-10-19

Peptides

Pyruvate carboxylase protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

Pyruvate carboxylase protein

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