SMTL ID : 2qf7.1

Crystal structure of a complete multifunctional pyruvate carboxylase from Rhizobium etli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.294, E.308, N.310 Ligands: AGS.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.294, A:E.308 MG.2: 3 residues within 4Å: Chain A: E.308, N.310 Ligands: AGS.8 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.308, A:E.308 MG.4: 4 residues within 4Å: Chain A: M.545, R.546, E.548, D.779 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.545, A:R.546, A:E.548, H2O.2, H2O.9 MG.11: 5 residues within 4Å: Chain B: E.294, E.308, N.310 Ligands: MG.12, AGS.16 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.294, B:E.294, B:E.308 MG.12: 4 residues within 4Å: Chain B: E.308, N.310 Ligands: MG.11, AGS.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.308, B:E.308, H2O.47 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:R.546, B:D.779, H2O.34, H2O.37 MG.19: 4 residues within 4Å: Chain C: E.294, E.308, N.310 Ligands: AGS.26 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.294, C:E.308 MG.20: 3 residues within 4Å: Chain C: E.308, N.310 Ligands: AGS.26 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.308, C:E.308 MG.22: 4 residues within 4Å: Chain C: M.545, R.546, E.548, D.779 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.545, C:R.546, C:E.548, H2O.53, H2O.59 MG.29: 5 residues within 4Å: Chain D: E.294, E.308, N.310 Ligands: MG.30, AGS.34 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.294, D:E.294, D:E.308 MG.30: 4 residues within 4Å: Chain D: E.308, N.310 Ligands: MG.29, AGS.34 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.308, D:E.308, H2O.97 MG.31: 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:R.546, D:D.779, H2O.85, H2O.88

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.560, K.729, H.758, H.760 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.560, A:H.758, A:H.760, H2O.13 ZN.10: 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.34 ZN.21: 4 residues within 4Å: Chain C: D.560, K.729, H.758, H.760 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.560, C:H.758, C:H.760, H2O.63 ZN.28: 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.84

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

CL.5: 4 residues within 4Å: Chain A: Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain B: Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain C: Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain C: G.74, P.75, I.76, E.77 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain D: Y.998, P.999, K.1000, V.1001 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain D: G.74, P.75, I.76, E.77 Ligand excluded by PLIP

2 x COA: COENZYME A(Non-covalent)

COA.7: 13 residues within 4Å: Chain A: R.438, R.480, Q.481, D.482, R.483, A.484, I.1037, K.1041, T.1042, L.1043, L.1065, N.1066 Chain B: F.55 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.481, A:D.482, A:R.483, A:T.1042, A:N.1066, B:D.58 Water bridges: A:R.385, A:D.482, B:R.54, B:S.60 Salt bridges: A:R.438, A:R.483 COA.25: 13 residues within 4Å: Chain C: R.438, R.480, Q.481, D.482, R.483, A.484, I.1037, K.1041, T.1042, L.1043, L.1065, N.1066 Chain D: F.55 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:D.58, C:Q.481, C:D.482, C:R.483, C:T.1042, C:N.1066 Water bridges: D:S.60, C:R.385, C:A.484 Salt bridges: C:R.438, C:R.483

4 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.8: 13 residues within 4Å: Chain A: V.222, H.227, Q.251, N.254, K.256, E.294, L.296, I.307, E.308, N.310, T.465 Ligands: MG.1, MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.222, A:H.227, A:Q.251, A:Q.251, A:N.254, A:E.308, A:N.310 AGS.16: 18 residues within 4Å: Chain B: M.175, K.177, M.187, E.219, K.220, V.222, H.227, Q.251, N.254, K.256, E.294, L.296, I.307, E.308, N.310, T.465 Ligands: MG.11, MG.12 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:K.220, B:V.222, B:H.227, B:Q.251, B:E.308, B:E.308, B:N.310, B:T.465 Salt bridges: B:K.177 AGS.26: 13 residues within 4Å: Chain C: V.222, H.227, Q.251, N.254, K.256, E.294, L.296, I.307, E.308, N.310, T.465 Ligands: MG.19, MG.20 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:V.222, C:H.227, C:Q.251, C:Q.251, C:N.254, C:E.308, C:N.310, C:T.465 AGS.34: 18 residues within 4Å: Chain D: M.175, K.177, M.187, E.219, K.220, V.222, H.227, Q.251, N.254, K.256, E.294, L.296, I.307, E.308, N.310, T.465 Ligands: MG.29, MG.30 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.219, D:K.220, D:V.222, D:H.227, D:Q.251, D:E.308, D:N.310, D:T.465, D:T.465 Salt bridges: D:K.177

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.9: 8 residues within 4Å: Chain A: R.31, L.394, D.395, G.396, G.397 Chain B: S.386, A.387, S.388 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.31, A:R.31, A:G.396, A:G.396, B:S.388 FMT.18: 8 residues within 4Å: Chain A: S.386, A.387, S.388 Chain B: R.31, L.394, D.395, G.396, G.397 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.31, B:R.31, B:G.396, A:S.386, A:S.388 FMT.27: 8 residues within 4Å: Chain C: R.31, L.394, D.395, G.396, G.397 Chain D: S.386, A.387, S.388 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:S.388, C:R.31, C:R.31, C:G.396, C:G.396 FMT.36: 8 residues within 4Å: Chain C: S.386, A.387, S.388 Chain D: R.31, L.394, D.395, G.396, G.397 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.386, C:S.388, D:R.31, D:R.31, D:G.396

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 5 residues within 4Å: Chain A: E.425 Chain B: L.36, H.334, P.344, G.347 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:E.425, A:E.425, B:G.347 Hydrogen bonds: B:P.344 GOL.35: 5 residues within 4Å: Chain C: E.425 Chain D: L.36, H.334, P.344, G.347 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:P.344 Water bridges: D:G.347, C:E.425, C:E.425

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

St Maurice, M. et al., Domain architecture of pyruvate carboxylase, a biotin-dependent multifunctional enzyme. Science (2007)

Release Date

2007-09-04

Peptides

Pyruvate carboxylase protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Pyruvate carboxylase protein