SMTL ID : 4emw.1

Crystal Structure of Staphylococcus aureus bound with the covalent inhibitor EtVC-CoA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 34 residues within 4Å: Chain A: V.6, G.7, V.9, A.10, G.11, F.31, E.32, K.33, D.34, 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, 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: CAJ.3 35 PLIP interactions: 32 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:N.41, A:P.45, A:L.129, A:V.158, A:V.158 Hydrogen bonds: A:A.10, A:G.11, 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:G.12, A:G.113, A:A.114, A:A.114, A:R.130, A:R.130, A:N.131, A:N.131, A:D.276, A:I.277, B:Y.418, B:Y.418 pi-Stacking: A:Y.157, A:Y.157 pi-Cation interactions: A:K.33 FAD.4: 33 residues within 4Å: Chain A: Y.418, A.419, P.420 Chain B: V.6, G.7, V.9, A.10, G.11, F.31, E.32, K.33, D.34, N.41, C.42, P.45, H.78, E.79, V.80, S.111, P.112, G.113, R.130, Y.157, V.158, N.241, F.244, G.275, D.276, P.292, L.293, A.294, A.297 Ligands: CAJ.7 30 PLIP interactions: 3 interactions with chain A, 27 interactions with chain B Hydrogen bonds: A:Y.418, B:G.7, B:A.10, B:G.11, B:K.33, B:D.34, B:N.41, B:N.41, B:V.80, B:V.80, B:S.111, B:G.113, B:N.241, B:D.276, B:P.292, B:A.294 Water bridges: A:Y.418, A:Y.418, B:V.9, B:G.12, B:A.114, B:N.131, B:N.131, B:I.277, B:W.295, B:A.297 Hydrophobic interactions: B:N.41, B:V.158 pi-Stacking: B:Y.157 pi-Cation interactions: B:K.33

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x CAJ: ethyl 5-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]pentanoate(Covalent)

CAJ.3: 25 residues within 4Å: Chain A: V.9, A.10, A.13, T.14, S.17, Q.18, R.21, S.38, F.39, A.40, N.41, C.42, A.60, Y.61, K.70, A.294, H.298 Chain B: Y.360, Y.418, P.425, K.426, M.431, Y.434, K.435 Ligands: FAD.1 22 PLIP interactions: 18 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.10, A:N.41, A:C.42, A:A.60, A:Y.61, A:A.294, B:Y.418, B:P.425 Hydrogen bonds: A:S.17, A:S.17, A:Q.18, A:Q.18, A:R.21, A:N.41, A:H.298, B:Y.418 Water bridges: A:K.70, A:K.70 Salt bridges: A:K.70, A:K.70, B:K.426 pi-Cation interactions: A:R.21 CAJ.7: 22 residues within 4Å: Chain A: Y.418, P.425, K.426, M.431, Y.434 Chain B: V.9, A.10, A.13, T.14, S.17, Q.18, R.21, S.38, F.39, A.40, N.41, C.42, Y.61, K.70, A.294, H.298 Ligands: FAD.4 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.61, B:A.294, A:Y.418 Hydrogen bonds: B:S.17, B:S.17, B:Q.18, B:Q.18, B:R.21, B:R.21, B:H.298 Salt bridges: B:K.70, A:K.426 pi-Cation interactions: B:R.21, B:R.21

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

CL.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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