SMTL ID : 4hnv.1

Crystal structure of R54E mutant of S. aureus Pyruvate carboxylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 15 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, E.301, L.303, E.313, T.470 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.227, A:I.229, A:H.234, A:Q.258 Salt bridges: A:K.142, A:K.142, A:K.184

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

MN.2: 4 residues within 4Å: Chain A: D.565, K.735, H.764, H.766 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.565, A:H.764 MN.5: 4 residues within 4Å: Chain B: D.565, K.735, H.764, H.766 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.565, B:H.764, B:H.766 MN.6: 4 residues within 4Å: Chain C: D.565, K.735, H.764, H.766 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.565, C:H.764, C:H.766 MN.11: 4 residues within 4Å: Chain D: D.565, K.735, H.764, H.766 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(Non-covalent)(Covalent)

BTI.3: 7 residues within 4Å: Chain A: K.1135 Chain B: N.498, G.503, F.504, P.505, F.611, K.613 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.1135, B:F.611 BTI.4: 9 residues within 4Å: Chain A: Y.495, N.498, G.503, F.504, P.505, F.611, K.613, F.1029 Chain B: K.1135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.611 BTI.8: 13 residues within 4Å: Chain C: Q.568, D.606, V.607, F.611, R.637, Y.644, G.860, Q.861, N.864, T.899, S.902, K.903 Chain D: K.1135 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.607 Hydrogen bonds: C:Y.644, C:Q.861, C:T.899, C:S.902, D:K.1135 BTI.10: 10 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, F.1029 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:V.499 Hydrogen bonds: D:F.611, D:K.613

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

ATP.7: 22 residues within 4Å: Chain C: K.142, M.182, K.184, G.188, G.189, G.190, 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 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:K.184, C:G.190, C:E.226, C:R.227, C:I.229, C:H.234, C:Q.258, C:H.261, C:E.301, C:E.301, C:N.315 Salt bridges: C:K.142, C:K.142, C:K.184, C:H.234, C:K.263

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

CL.9: 4 residues within 4Å: Chain A: K.777, Q.778 Chain D: K.777, Q.778 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, L.P. et al., Characterizing the Importance of the Biotin Carboxylase Domain Dimer for Staphylococcus aureus Pyruvate Carboxylase Catalysis. Biochemistry (2013)

Release Date

2013-01-16

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Pyruvate carboxylase