SMTL ID : 8gk8.1

R21A Staphylococcus aureus pyruvate carboxylase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

homo-tetramer

Ligands

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

BTI.1: 10 residues within 4Å: Chain A: K.1112 Chain C: Y.472, N.475, V.476, G.480, F.481, P.482, F.588, K.590, F.1006 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.472, C:V.476 Hydrogen bonds: C:F.588, C:K.590 BTI.4: 11 residues within 4Å: Chain A: Y.472, N.475, V.476, G.480, F.481, P.482, N.587, F.588, K.590, F.1006 Chain C: K.1112 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:K.1112, A:N.475, A:N.587, A:K.590 Hydrophobic interactions: A:Y.472, A:N.475, A:V.476 BTI.5: 12 residues within 4Å: Chain B: K.1112 Chain D: Y.472, N.475, V.476, N.479, G.480, F.481, P.482, F.588, K.590, L.998, F.1006 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:N.475, D:V.476 Hydrogen bonds: D:F.588, D:K.590 BTI.8: 12 residues within 4Å: Chain B: Y.472, N.475, V.476, G.480, F.481, P.482, N.587, F.588, K.590, Y.995, F.1006 Chain D: K.1112 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.472, B:Y.995 Hydrogen bonds: B:N.587

1 x COA: COENZYME A(Non-covalent)

COA.2: 24 residues within 4Å: Chain A: R.367, R.417, E.418, R.420, R.422, S.462, L.463, D.464, R.465, G.466, I.1020, G.1023, K.1024, R.1025, M.1048, N.1049, R.1053 Chain D: R.44, Y.45, K.46, A.47, D.48, E.49, S.50 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:R.420, A:L.463, A:D.464, A:R.465, A:N.1049, D:K.46, D:A.47 Salt bridges: A:R.367, A:R.420, A:R.422, A:R.422, A:R.465, A:R.1053

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

MN.3: 3 residues within 4Å: Chain A: D.542, H.741, H.743 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.542, A:H.741 MN.6: 4 residues within 4Å: Chain B: D.542, K.712, H.741, H.743 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.542, B:H.741, B:H.743 MN.7: 4 residues within 4Å: Chain C: D.542, K.712, H.741, H.743 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.542, C:H.741 MN.10: 4 residues within 4Å: Chain D: D.542, K.712, H.741, H.743 No protein-ligand interaction detected (PLIP)

1 x ACO: ACETYL COENZYME *A(Covalent)

ACO.9: 22 residues within 4Å: Chain A: F.20, A.21, R.44, Y.45, K.46, A.47, D.48, E.49, S.50 Chain D: R.367, E.418, R.420, R.422, S.462, L.463, D.464, R.465, G.466, K.1024, R.1025, N.1049, R.1053 16 PLIP interactions: 12 interactions with chain D, 4 interactions with chain A Hydrogen bonds: D:R.420, D:S.462, D:D.464, D:R.465, D:G.466, D:K.1024, D:N.1049, A:K.46, A:A.47, A:S.50 Salt bridges: D:R.367, D:R.422, D:R.422, D:R.465, D:R.1053 Hydrophobic interactions: A:F.20

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laseke, A.J. et al., Allosteric Site at the Biotin Carboxylase Dimer Interface Mediates Activation and Inhibition in Staphylococcus aureus Pyruvate Carboxylase. Biochemistry (2023)

Release Date

2023-08-30

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
D

D
A

Pyruvate carboxylase