SMTL ID : 4dki.3 (2 other biounits)

Structural Insights into the Anti- Methicillin-Resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x RB6: (2R)-2-[(1R)-1-{[(2Z)-2-(5-amino-1,2,4-thiadiazol-3-yl)-2-(hydroxyimino)acetyl]amino}-2-oxoethyl]-5-({2-oxo-1-[(3R)-pyr rolidin-3-yl]-2,5-dihydro-1H-pyrrol-3-yl}methyl)-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid(Covalent)

RB6.1: 15 residues within 4Å: Chain A: S.381, K.384, Y.424, S.440, N.442, G.498, Q.499, K.575, S.576, G.577, T.578, A.579, E.580, M.619, A.620 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.578, A:M.619 Hydrogen bonds: A:S.378, A:S.378, A:S.381, A:S.440, A:S.440, A:S.440, A:N.442, A:Q.499, A:T.578, A:T.578, A:T.578 Salt bridges: A:H.561, A:K.575 pi-Stacking: A:Y.424 RB6.10: 14 residues within 4Å: Chain B: S.381, K.384, Y.424, S.440, N.442, Y.497, G.498, Q.499, S.576, G.577, T.578, A.579, E.580, A.620 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.424, B:Y.424 Hydrogen bonds: B:S.381, B:S.440, B:S.440, B:S.440, B:N.442, B:G.498, B:Q.499, B:S.576, B:T.578, B:T.578, B:E.580 Salt bridges: B:H.561, B:K.575 pi-Stacking: B:Y.424

4 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.2: 4 residues within 4Å: Chain A: R.129, T.143, R.219, V.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.143, A:R.219 BCT.3: 4 residues within 4Å: Chain A: D.106, H.107, Q.115, K.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.106, A:H.107, A:K.116, A:K.116 BCT.4: 4 residues within 4Å: Chain A: K.131, D.301 Chain B: K.131, D.301 No protein-ligand interaction detected (PLIP) BCT.11: 3 residues within 4Å: Chain B: D.13, E.16, R.61 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.16, B:R.61

7 x CD: CADMIUM ION(Non-covalent)

CD.5: 5 residues within 4Å: Chain A: H.121, E.123 Chain B: E.123 Ligands: CL.8, CD.12 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:H.121, A:E.123, B:E.123, B:E.123 CD.6: 1 residues within 4Å: Chain A: H.210 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.210 CD.7: 4 residues within 4Å: Chain A: G.113, H.289 Chain B: D.187 Ligands: CL.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Metal complexes: A:G.113, A:H.289, B:D.187, B:D.187 CD.12: 6 residues within 4Å: Chain A: E.123 Chain B: H.121, E.123, N.285 Ligands: CD.5, CL.16 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.121, B:E.123, A:E.123, A:E.123 CD.13: 5 residues within 4Å: Chain A: D.187 Chain B: G.113, Q.115, H.289 Ligands: CL.17 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Metal complexes: B:G.113, B:H.289, A:D.187, A:D.187 CD.14: 1 residues within 4Å: Chain B: H.210 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.210 CD.15: 2 residues within 4Å: Chain B: N.547, D.551 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.551, B:D.551

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

CL.8: 6 residues within 4Å: Chain A: H.121, E.123, T.278, V.280 Chain B: E.123 Ligands: CD.5 Ligand excluded by PLIP CL.9: 8 residues within 4Å: Chain A: G.113, Q.115, Q.118, A.288, H.289 Chain B: Q.185, D.187 Ligands: CD.7 Ligand excluded by PLIP CL.16: 7 residues within 4Å: Chain A: E.123 Chain B: H.121, E.123, R.276, T.278, V.280 Ligands: CD.12 Ligand excluded by PLIP CL.17: 8 residues within 4Å: Chain A: Q.185, D.187 Chain B: G.113, Q.115, Q.118, A.288, H.289 Ligands: CD.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lovering, A.L. et al., Structural Insights into the Anti-methicillin-resistant Staphylococcus aureus (MRSA) Activity of Ceftobiprole. J.Biol.Chem. (2012)

Release Date

2012-08-01

Peptides

Penicillin-binding protein 2': AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Penicillin-binding protein 2'

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