SMTL ID : 4m6v.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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.1 ZN.8: 5 residues within 4Å: Chain B: D.114, K.283, H.312, H.314, Q.348 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.114, B:H.312, B:H.314, H2O.6 ZN.14: 5 residues within 4Å: Chain C: D.114, K.283, H.312, H.314, Q.348 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.114, C:H.312, C:H.314, H2O.9 ZN.21: 5 residues within 4Å: Chain D: D.114, K.283, H.312, H.314, Q.348 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.114, D:H.312, D:H.314, H2O.12

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.9: 4 residues within 4Å: Chain B: M.99, R.100, E.102, D.333 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.99, B:R.100, B:E.102, B:D.333, H2O.6, H2O.8 MG.16: 4 residues within 4Å: Chain C: M.99, R.100, E.102, D.333 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.99, C:R.100, C:D.333, H2O.10, H2O.11 MG.22: 5 residues within 4Å: Chain D: M.99, R.100, E.102, R.302, D.333 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:M.99, D:E.102, D:D.333, H2O.14, H2O.14

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

CL.3: 4 residues within 4Å: Chain A: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain C: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.23: 4 residues within 4Å: Chain D: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.4: 10 residues within 4Å: Chain A: R.113, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, V.446, T.447 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.446 Hydrogen bonds: A:R.113, A:R.113, A:Q.117, A:A.152 Water bridges: A:G.408 Salt bridges: A:R.113, A:R.186 PYR.11: 10 residues within 4Å: Chain B: 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 B Hydrophobic interactions: B:L.184 Hydrogen bonds: B:R.113, B:R.113, B:Q.117, B:A.152 Salt bridges: B:R.113, B:R.186 PYR.18: 9 residues within 4Å: Chain C: R.113, 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:R.113, C:R.113, C:Q.117, C:Q.117, C:A.152, C:T.447 Salt bridges: C:R.186 PYR.24: 10 residues within 4Å: Chain D: R.113, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, V.446, T.447 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.446 Hydrogen bonds: D:R.113, D:R.113, D:Q.117, D:Q.117, D:A.152, D:T.447 Salt bridges: D:R.186

8 x BYT: Biocytin(Non-covalent)

BYT.5: 12 residues within 4Å: Chain A: Y.44, D.47, V.48, G.52, H.53, P.54, R.159, F.160, T.162, A.562, Y.566, R.631 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.160, A:A.562, A:Y.566 Hydrogen bonds: A:G.52, A:T.162 Salt bridges: A:R.159 BYT.6: 8 residues within 4Å: Chain A: E.55, R.59, A.121, R.123, F.389, T.411, N.412, E.415 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.59 Water bridges: A:A.121, A:F.389 BYT.12: 12 residues within 4Å: Chain B: Y.44, D.47, V.48, G.52, H.53, P.54, R.159, F.160, T.162, A.562, Y.566, R.631 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.160, B:A.562, B:Y.566 Hydrogen bonds: B:G.52 Salt bridges: B:R.159 BYT.13: 7 residues within 4Å: Chain B: R.59, A.121, R.123, F.389, T.411, N.412, E.415 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.59 Water bridges: B:A.121, B:A.121 BYT.19: 12 residues within 4Å: Chain C: Y.44, D.47, V.48, G.52, H.53, P.54, R.159, F.160, T.162, A.562, Y.566, R.631 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.160, C:T.162, C:A.562, C:Y.566 Hydrogen bonds: C:G.52 Salt bridges: C:R.159 BYT.20: 9 residues within 4Å: Chain C: E.55, R.59, A.121, R.123, F.389, E.390, T.411, N.412, E.415 3 PLIP interactions: 3 interactions with chain C Water bridges: C:A.121, C:A.121, C:F.389 BYT.25: 13 residues within 4Å: Chain D: Y.44, D.47, V.48, N.51, G.52, H.53, P.54, R.159, F.160, T.162, A.562, Y.566, R.631 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.160, D:A.562, D:Y.566 Hydrogen bonds: D:G.52, D:T.162 Salt bridges: D:R.159 BYT.26: 7 residues within 4Å: Chain D: R.59, A.121, R.123, F.389, T.411, N.412, E.415 3 PLIP interactions: 3 interactions with chain D Water bridges: D:A.121, D:A.121, D:F.389

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: D.315, G.318, G.344, N.345, P.396 Chain B: D.315, G.318, G.344, N.345 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.315, A:N.345, A:N.345, B:D.315, B:N.345 GOL.15: 9 residues within 4Å: Chain C: D.315, G.318, G.344, N.345 Chain D: D.315, G.318, G.344, N.345, P.396 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.315, C:N.345, C:N.345, D:D.315, D:N.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lietzan, A.D. et al., The role of biotin and oxamate in the carboxyltransferase reaction of pyruvate carboxylase. Arch.Biochem.Biophys. (2014)

Release Date

2014-09-10

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