SMTL ID : 3bg5.1 (2 other biounits)

Crystal Structure of Staphylococcus Aureus Pyruvate Carboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: D.565, K.735, H.764, H.766 Ligands: PYR.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.565, A:H.764, A:H.766 MN.5: 5 residues within 4Å: Chain B: D.565, K.735, H.764, H.766 Ligands: PYR.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.565, B:H.764, B:H.766 MN.8: 5 residues within 4Å: Chain C: D.565, K.735, H.764, H.766 Ligands: PYR.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.565, C:H.764, C:H.766 MN.12: 5 residues within 4Å: Chain D: D.565, K.735, H.764, H.766 Ligands: PYR.14 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.565, D:H.764, D:H.766

4 x BTI: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL(Covalent)

BTI.2: 11 residues within 4Å: Chain A: K.1135 Chain B: Y.495, N.498, G.503, F.504, P.505, F.611, K.613, L.1021, F.1029, E.1083 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.611 BTI.6: 11 residues within 4Å: Chain A: Y.495, N.498, V.499, G.503, F.504, P.505, F.611, K.613, L.1021, F.1029 Chain B: K.1135 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.499 Hydrogen bonds: A:N.610, A:K.613 BTI.9: 11 residues within 4Å: Chain C: K.1135 Chain D: Y.495, N.498, V.499, G.503, F.504, P.505, F.611, K.613, L.1021, F.1029 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.495, D:V.499 Hydrogen bonds: D:F.611 BTI.13: 13 residues within 4Å: Chain C: Q.568, D.606, F.611, R.637, Y.644, G.860, Q.861, N.864, T.899, S.902, K.903 Chain D: K.1135 Ligands: PYR.10 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:N.864 Hydrogen bonds: C:Y.644, C:Q.861, C:T.899, C:S.902, C:K.903

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.3: 8 residues within 4Å: Chain A: R.564, D.565, Q.568, L.635, F.670, K.735, T.899 Ligands: MN.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.564, A:R.564, A:Q.568, A:K.735, A:T.899 Salt bridges: A:K.735 PYR.7: 9 residues within 4Å: Chain B: R.564, D.565, Q.568, L.635, R.637, K.735, V.898, T.899 Ligands: MN.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.564, B:R.564, B:Q.568, B:K.735, B:T.899 Salt bridges: B:R.637, B:K.735 PYR.10: 11 residues within 4Å: Chain C: R.564, D.565, Q.568, G.602, L.635, R.637, F.670, K.735, T.899 Ligands: MN.8, BTI.13 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.564, C:R.564, C:Q.568, C:Q.568, C:K.735, C:T.899 Salt bridges: C:R.564, C:R.637, C:K.735 PYR.14: 7 residues within 4Å: Chain D: Q.568, L.635, R.637, F.670, K.735, T.899 Ligands: MN.12 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.568, D:K.735 Salt bridges: D:R.637, D:K.735

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 16 residues within 4Å: Chain A: K.142, I.157, M.182, K.184, E.226, R.227, Y.228, I.229, H.234, Q.258, H.261, K.263, E.301, L.303, E.313, N.315 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:K.184, A:S.187, A:R.227, A:I.229, A:H.234, A:Q.258, A:N.315, A:N.315, A:R.317 Salt bridges: A:K.142, A:K.142, A:K.184, A:H.261, A:H.261, A:K.263 ATP.11: 21 residues within 4Å: Chain C: K.142, M.182, K.184, G.188, G.189, G.191, M.194, E.226, R.227, Y.228, I.229, H.234, Q.258, H.261, K.263, E.301, L.303, I.312, E.313, N.315, T.470 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:K.184, C:G.188, C:G.189, C:G.189, C:E.226, C:R.227, C:I.229, C:H.234, C:Q.258, C:H.261, C:E.301, C:E.313, C:N.315, C:T.470, C:T.470 Salt bridges: C:K.142, C:K.142, C:K.184, C:K.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, S. et al., Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction. Nat.Struct.Mol.Biol. (2008)

Release Date

2008-02-26

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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