SMTL ID : 4mfd.1

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with oxalate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.114, K.283, H.312, H.314, Q.348 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.114, A:H.312, A:H.314, H2O.4 ZN.6: 5 residues within 4Å: Chain B: D.114, K.283, H.312, H.314, Q.348 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.114, B:D.114, B:H.312, B:H.314, H2O.6 ZN.11: 6 residues within 4Å: Chain C: R.113, D.114, K.283, H.312, H.314, Q.348 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.114, C:D.114, C:H.312, C:H.314 ZN.15: 5 residues within 4Å: Chain D: D.114, K.283, H.312, H.314, Q.348 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.114, D:D.114, D:H.312, D:H.314, H2O.8

4 x OXL: OXALATE ION(Non-covalent)

OXL.2: 9 residues within 4Å: Chain A: R.113, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, T.447 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.117, A:A.152, A:T.447, A:T.447, A:T.447 Water bridges: A:R.113, A:R.113 Salt bridges: A:R.113, A:R.113, A:R.186 OXL.7: 9 residues within 4Å: Chain B: R.113, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, T.447 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.117, B:T.447, B:T.447, B:T.447 Water bridges: B:R.113 Salt bridges: B:R.113, B:R.113, B:R.186 OXL.12: 10 residues within 4Å: Chain C: R.113, D.114, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, T.447 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.117, C:Q.117, C:Q.117, C:T.447 Salt bridges: C:R.113, C:R.113, C:R.186 OXL.16: 10 residues within 4Å: Chain D: R.113, D.114, Q.117, G.151, A.152, L.184, R.186, K.283, V.446, T.447 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.117, D:A.152, D:T.447, D:T.447 Water bridges: D:R.113 Salt bridges: D:R.113, D:R.113, D:R.186

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: M.99, R.100, E.102, D.333 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:M.99, A:R.100, A:E.102, A:D.333, H2O.2 MG.8: 5 residues within 4Å: Chain B: M.99, R.100, E.102, R.302, D.333 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:M.99, B:R.100, B:E.102, B:D.333, H2O.5 MG.13: 5 residues within 4Å: Chain C: M.99, R.100, E.102, D.333, R.363 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:M.99, C:R.100, C:E.102, C:D.333, H2O.6 MG.17: 5 residues within 4Å: Chain D: M.99, R.100, E.102, D.333, R.363 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:M.99, D:R.100, D:E.102, D:D.333, H2O.7

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

CL.4: 4 residues within 4Å: Chain A: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain B: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.18: 4 residues within 4Å: Chain D: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: D.315, G.344, N.345 Chain C: D.315, G.318, G.344, N.345 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:D.315, A:N.345, C:D.315, C:N.345, C:N.345 GOL.10: 8 residues within 4Å: Chain B: D.315, G.318, G.344, N.345 Chain D: D.315, G.318, G.344, N.345 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:D.315, D:N.345, B:D.315, B:N.345, B:N.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lietzan, A.D. et al., Insights into the carboxyltransferase reaction of pyruvate carboxylase from the structures of bound product and intermediate analogs. Biochem.Biophys.Res.Commun. (2013)

Release Date

2013-11-13

Peptides

PYRUVATE CARBOXYLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PYRUVATE CARBOXYLASE

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