SMTL ID : 4loc.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 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.7 ZN.7: 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.12 ZN.11: 5 residues within 4Å: Chain C: R.113, D.114, K.283, H.312, H.314 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.114, C:H.312, C:H.314, H2O.15 ZN.17: 5 residues within 4Å: Chain D: R.113, D.114, K.283, H.312, H.314 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.114, D:H.312, D:H.314, H2O.20

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: M.99, R.100, E.102, D.333 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:M.99, A:R.100, A:E.102, A:D.333, H2O.3, H2O.7 MG.8: 4 residues within 4Å: Chain B: M.99, R.100, E.102, D.333 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.99, B:R.100, B:E.102, H2O.10, H2O.11 MG.12: 4 residues within 4Å: Chain C: M.99, R.100, E.102, D.333 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.99, C:R.100, C:E.102, C:D.333, H2O.14, H2O.15 MG.18: 5 residues within 4Å: Chain D: M.99, R.100, N.101, E.102, D.333 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:M.99, D:R.100, D:D.333, H2O.19, H2O.20

3 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.14: 4 residues within 4Å: Chain C: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain D: Y.552, P.553, K.554, V.555 Ligand excluded by PLIP

4 x BTN: BIOTIN(Non-covalent)

BTN.4: 13 residues within 4Å: Chain A: Y.44, D.47, V.48, N.51, G.52, H.53, P.54, R.159, F.160, T.162, Y.566, Y.577, R.631 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.52, A:T.162, A:Y.577 Salt bridges: A:H.53 BTN.9: 9 residues within 4Å: Chain B: Y.44, D.47, G.52, P.54, F.160, T.162, Y.566, Y.577, R.631 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.54 Hydrogen bonds: B:G.52, B:Y.577 BTN.15: 9 residues within 4Å: Chain C: D.47, N.51, G.52, P.54, R.159, T.162, A.562, Y.566, R.631 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:A.562, C:Y.566 Hydrogen bonds: C:G.52 BTN.20: 11 residues within 4Å: Chain D: Y.44, D.47, V.48, N.51, G.52, H.53, P.54, R.159, T.162, Y.566, R.631 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.52, D:T.162 Salt bridges: D:H.53

4 x OXM: OXAMIC ACID(Non-covalent)

OXM.5: 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.113, A:R.113, A:Q.117, A:Q.117, A:A.152, A:T.447, A:T.447 Salt bridges: A:R.113, A:R.186 OXM.10: 11 residues within 4Å: Chain B: R.113, D.114, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, V.446, T.447 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.113, B:R.113, B:Q.117, B:Q.117, B:A.152, B:T.447, B:T.447 Salt bridges: B:R.113, B:R.186 OXM.16: 9 residues within 4Å: Chain C: R.113, Q.117, G.151, A.152, L.184, R.186, F.219, K.283, T.447 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.113, C:R.113, C:Q.117, C:Q.117, C:A.152, C:T.447, C:T.447 Salt bridges: C:R.113, C:R.186 OXM.21: 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 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:R.113, D:R.113, D:Q.117, D:Q.117, D:A.152, D:T.447, D:T.447 Water bridges: D:T.447 Salt bridges: D:R.113, D:R.186

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: D.315, G.318, G.344, N.345 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.13: 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 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:D.315, D:N.345, C:D.315, C:N.345, C:N.345 Water bridges: C:G.318

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

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