SMTL ID : 4eqr.1

Crystal structure of the Y361F mutant of Staphylococcus aureus CoADR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: T.353 Ligands: COA.5 No protein-ligand interaction detected (PLIP)

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

CL.2: 6 residues within 4Å: Chain A: A.40, N.41, C.42, A.43 Chain B: F.360 Ligands: COA.5 Ligand excluded by PLIP CL.3: 1 residues within 4Å: Chain A: P.259 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: N.84, D.85, E.86, R.87 Ligand excluded by PLIP CL.7: 6 residues within 4Å: Chain A: F.360 Chain B: A.40, N.41, C.42, A.43 Ligands: COA.12 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: V.352, T.353, K.435 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: N.84, D.85, E.86, R.87 Ligand excluded by PLIP

2 x COA: COENZYME A(Non-covalent)

COA.5: 26 residues within 4Å: Chain A: V.9, A.10, A.13, T.14, S.17, Q.18, R.21, S.38, F.39, N.41, C.42, A.60, Y.61, F.66, K.70, A.294, H.298 Chain B: Y.418, P.425, K.426, M.431, Y.434, K.435 Ligands: CL.2, FAD.6, MG.9 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.9, A:A.60, A:Y.61, A:F.66 Hydrogen bonds: A:T.14, A:S.17, A:Q.18, A:Q.18, A:R.21, A:R.21, A:N.41 Water bridges: A:K.70, A:K.70, A:H.298, B:K.426 Salt bridges: A:K.70, B:K.426 pi-Cation interactions: A:R.21, A:R.21 COA.12: 23 residues within 4Å: Chain A: Y.418, P.425, M.431, Y.434 Chain B: V.9, A.10, A.13, T.14, S.17, Q.18, R.21, S.38, F.39, N.41, C.42, A.60, Y.61, F.66, K.70, A.294, H.298 Ligands: CL.7, FAD.13 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.13, B:A.60, B:Y.61, B:F.66 Hydrogen bonds: B:S.17, B:S.17, B:Q.18, B:Q.18, B:R.21, B:N.41, B:Y.61 Water bridges: B:R.21 Salt bridges: B:R.21, B:K.70, B:K.70 pi-Cation interactions: B:R.21, B:R.21

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.6: 37 residues within 4Å: Chain A: V.6, G.7, V.9, A.10, G.11, G.12, F.31, E.32, K.33, D.34, F.39, N.41, C.42, P.45, H.78, E.79, V.80, S.111, P.112, G.113, L.129, R.130, Y.157, V.158, E.161, N.241, F.244, G.275, D.276, P.292, L.293, A.294, A.297 Chain B: Y.418, A.419, P.420 Ligands: COA.5 31 PLIP interactions: 30 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.45, A:L.129, A:V.158, A:V.158 Hydrogen bonds: A:G.7, A:A.10, A:G.11, A:G.12, A:K.33, A:D.34, A:D.34, A:N.41, A:N.41, A:V.80, A:V.80, A:S.111, A:D.276, A:P.292, A:A.294, B:Y.418 Water bridges: A:V.9, A:K.33, A:A.114, A:A.114, A:A.114, A:A.114, A:N.131, A:I.277, A:A.297 pi-Stacking: A:Y.157 pi-Cation interactions: A:K.33 FAD.13: 37 residues within 4Å: Chain A: Y.418, A.419, P.420 Chain B: V.6, G.7, V.9, A.10, G.11, G.12, F.31, E.32, K.33, D.34, F.39, N.41, C.42, P.45, H.78, E.79, V.80, S.111, P.112, G.113, L.129, R.130, Y.157, V.158, E.161, N.241, F.244, G.275, D.276, P.292, L.293, A.294, A.297 Ligands: COA.12 28 PLIP interactions: 27 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:P.45, B:L.129, B:V.158 Hydrogen bonds: B:G.7, B:A.10, B:G.11, B:G.12, B:K.33, B:D.34, B:N.41, B:N.41, B:V.80, B:V.80, B:S.111, B:D.276, B:P.292, B:A.294, A:Y.418 Water bridges: B:V.9, B:K.33, B:N.131, B:N.131, B:D.276, B:I.277, B:W.295, B:A.297 pi-Stacking: B:Y.157 pi-Cation interactions: B:K.33

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wallace, B.D. et al., Turnover-Dependent Covalent Inactivation of Staphylococcus aureus Coenzyme A-Disulfide Reductase by Coenzyme A-Mimetics: Mechanistic and Structural Insights. Biochemistry (2012)

Release Date

2012-10-17

Peptides

Coenzyme A disulfide reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Coenzyme A disulfide reductase