SMTL ID : 3ho8.1

Crystal Structure of S. aureus Pyruvate Carboxylase in complex with Coenzyme A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-tetramer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 23 residues within 4Å: Chain A: R.367, R.417, E.418, R.420, R.422, S.462, L.463, R.465, G.466, G.1023, K.1024, R.1025, M.1048, N.1049, R.1053 Chain C: A.24, R.44, Y.45, K.46, A.47, D.48, E.49, S.50 15 PLIP interactions: 3 interactions with chain C, 12 interactions with chain A Hydrogen bonds: C:D.48, C:D.48, C:S.50, A:R.420, A:R.420, A:L.463, A:L.463, A:D.464, A:R.465, A:K.1024 Salt bridges: A:R.367, A:R.420, A:R.422, A:R.422, A:R.1053 COA.3: 21 residues within 4Å: Chain B: R.367, R.417, E.418, R.420, R.422, S.462, L.463, R.465, G.466, G.1023, K.1024, R.1025, L.1026, M.1048 Chain D: R.44, Y.45, K.46, A.47, D.48, E.49, S.50 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.367, B:R.420, B:L.463, B:R.465, B:R.465, B:K.1024, B:N.1049, B:R.1053, D:A.47 Salt bridges: B:R.367, B:R.420, B:R.422, B:R.422, B:R.465, B:K.1024 COA.5: 26 residues within 4Å: Chain A: A.24, R.44, Y.45, K.46, A.47, D.48, E.49, S.50 Chain C: R.367, R.414, E.418, R.420, R.422, S.462, L.463, D.464, R.465, G.466, I.1020, G.1023, K.1024, R.1025, L.1026, M.1048, N.1049, R.1053 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.420, C:R.420, C:L.463, C:D.464, C:R.465, C:K.1024, C:K.1024, C:N.1049, A:S.50 Salt bridges: C:R.367, C:R.420, C:R.422, C:R.422, C:R.465, C:R.1053 COA.8: 23 residues within 4Å: Chain B: A.24, R.44, Y.45, K.46, A.47, D.48, S.50 Chain D: R.367, R.417, E.418, R.420, R.422, S.462, L.463, D.464, R.465, G.466, G.1023, K.1024, R.1025, L.1026, N.1049, R.1053 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:R.367, D:R.420, D:R.420, D:S.462, D:S.462, D:D.464, D:R.465, D:K.1024, D:K.1024, B:S.50 Salt bridges: D:R.367, D:R.420, D:R.422, D:R.422, D:R.465, D:R.465, D:R.1053

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

MN.2: 5 residues within 4Å: Chain A: D.542, K.712, H.741, H.743, Q.777 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.542, A:H.741, A:H.743 MN.4: 5 residues within 4Å: Chain B: R.541, 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.6: 4 residues within 4Å: Chain C: D.542, K.712, H.741, H.743 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.542, C:H.741, C:H.743 MN.9: 4 residues within 4Å: Chain D: D.542, K.712, H.741, H.743 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.542, D:H.741, D:H.743

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

BTI.7: 11 residues within 4Å: Chain C: Y.472, N.475, V.476, N.479, G.480, F.481, P.482, N.587, F.588, K.590, F.1006 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.476 Hydrogen bonds: C:F.588 BTI.10: 12 residues within 4Å: Chain D: Y.472, N.475, V.476, N.479, G.480, F.481, P.482, N.587, F.588, K.590, L.998, F.1006 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.476 Hydrogen bonds: D:N.587

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, L.P. et al., A Symmetrical Tetramer for S. aureus Pyruvate Carboxylase in Complex with Coenzyme A. Structure (2009)

Release Date

2009-06-30

Peptides

Pyruvate carboxylase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
C

D
B

Pyruvate carboxylase