SMTL ID : 4c12.1

X-ray Crystal Structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys and ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: L.201, M.212, E.213, G.216, F.244 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.213 GOL.2: 5 residues within 4Å: Chain A: E.213, H.217, F.244, Y.247 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.213, A:H.217, A:H.217 GOL.7: 6 residues within 4Å: Chain B: L.201, M.212, E.213, G.216, F.244 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.213 GOL.8: 5 residues within 4Å: Chain B: E.213, H.217, F.244, Y.247 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.213, B:H.217, B:H.217

2 x UML: Uridine 5'Diphospho N-acetyl muramoyl-L-Alanyl-D-Glutamyl-L-Lysine(Non-covalent)

UML.3: 28 residues within 4Å: Chain A: T.28, D.29, S.30, R.31, F.39, S.42, G.44, Y.45, T.46, V.47, S.49, F.52, A.150, N.151, T.152, T.153, E.155, S.179, H.181, R.187, H.205, Y.351, H.353, R.383, D.406, N.407, S.456, E.460 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Y.45, A:F.52 Hydrogen bonds: A:T.28, A:T.28, A:S.30, A:S.30, A:S.42, A:Y.45, A:T.46, A:T.46, A:V.47, A:S.49, A:N.151, A:N.151, A:T.152, A:T.152, A:T.153, A:S.179, A:R.187, A:R.187, A:R.383, A:E.460 Water bridges: A:T.152, A:E.155, A:H.205 Salt bridges: A:R.187, A:R.383 UML.9: 28 residues within 4Å: Chain B: T.28, D.29, S.30, R.31, F.39, S.42, G.44, Y.45, T.46, V.47, S.49, F.52, A.150, N.151, T.152, T.153, E.155, S.179, H.181, R.187, H.205, Y.351, H.353, R.383, D.406, N.407, S.456, E.460 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:Y.45, B:F.52 Hydrogen bonds: B:T.28, B:D.29, B:S.30, B:S.30, B:S.42, B:Y.45, B:T.46, B:T.46, B:T.46, B:V.47, B:S.49, B:N.151, B:N.151, B:T.152, B:T.153, B:S.179, B:R.187, B:R.187, B:R.383, B:E.460 Water bridges: B:T.28, B:T.152, B:T.152, B:E.155, B:H.205 Salt bridges: B:R.187, B:R.383

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.4: 21 residues within 4Å: Chain A: G.110, T.111, N.112, G.113, K.114, T.115, S.116, E.177, N.200, F.300, N.304, R.335, D.350, Y.351, A.352, H.353, D.356, G.357, K.360, L.361 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:G.113, A:G.113, A:K.114, A:T.115, A:S.116, A:N.200, A:N.304, A:N.304, A:D.350, A:Y.351 Water bridges: A:K.114, A:K.114, A:T.115, A:N.239, A:R.335 Salt bridges: A:K.114, A:R.335 ADP.10: 21 residues within 4Å: Chain B: G.110, T.111, N.112, G.113, K.114, T.115, S.116, E.177, N.200, F.300, N.304, R.335, D.350, Y.351, A.352, H.353, D.356, G.357, K.360, L.361 Ligands: MG.11 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.113, B:G.113, B:K.114, B:T.115, B:T.115, B:S.116, B:N.200, B:N.304, B:N.304, B:D.350, B:Y.351 Water bridges: B:K.114, B:K.114, B:N.239, B:R.335, B:R.335 Salt bridges: B:K.114, B:R.335

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: T.115, T.137, E.177 Ligands: ADP.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.115, A:T.137, A:E.177, H2O.6, H2O.7 MG.6: 7 residues within 4Å: Chain A: G.110, T.111, K.114, D.204, H.205, Y.215, K.219 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.111, A:H.205 MG.11: 4 residues within 4Å: Chain B: T.115, T.137, E.177 Ligands: ADP.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.115, B:T.137, B:E.177, H2O.25, H2O.26 MG.12: 7 residues within 4Å: Chain B: G.110, T.111, K.114, D.204, H.205, Y.215, K.219 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.111, B:H.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruane, K.M. et al., Specificity Determinants for Lysine Incorporation in Staphylococcus Aureus Peptidoglycan as Revealed by the Structure of a Mure Enzyme Ternary Complex. J.Biol.Chem. (2013)

Release Date

2013-10-02

Peptides

UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE

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