SMTL ID : 4c13.1

x-ray crystal structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: N.240, S.258 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: N.240, S.258 Ligand excluded by PLIP

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: K.114, T.115, T.137, E.177 Ligands: PO4.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.115, A:T.137, A:E.177 MG.3: 7 residues within 4Å: Chain A: G.110, T.111, K.114, D.204, H.205, Y.215, K.219 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.205, H2O.2 MG.8: 5 residues within 4Å: Chain B: K.114, T.115, T.137, E.177 Ligands: PO4.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.115, B:T.137, B:E.177 MG.9: 7 residues within 4Å: Chain B: G.110, T.111, K.114, D.204, H.205, Y.215, K.219 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.205, H2O.10

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

UML.4: 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, 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, K.457, E.460 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:Y.45, A:V.47, A:F.52 Hydrogen bonds: A:T.28, A:D.29, A:D.29, A:S.30, A:S.30, A:S.42, A:Y.45, A:T.46, A:T.46, A:T.46, A:V.47, A:V.47, A:N.151, A:N.151, A:T.152, A:T.153, A:S.179, A:S.179, A:R.187, A:R.187, A:R.383, A:E.460 Water bridges: A:T.28, A:S.49, A:E.155, A:H.205 Salt bridges: A:R.187, A:R.383 pi-Cation interactions: A:R.31 UML.10: 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, 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, K.457, E.460 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:Y.45, B:V.47, B:F.52 Hydrogen bonds: B:T.28, 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:V.47, B:V.47, B:N.151, B:N.151, B:T.152, B:T.152, B:T.153, B:S.179, B:S.179, B:R.187, B:R.187, B:R.383, B:E.460 Water bridges: B:S.49, B:E.155 Salt bridges: B:R.187, B:R.383 pi-Cation interactions: B:R.31

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 8 residues within 4Å: Chain A: N.112, G.113, K.114, T.115, S.116, R.335, Y.351 Ligands: MG.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.113, A:K.114, A:T.115, A:T.115, A:S.116 Water bridges: A:S.116 Salt bridges: A:R.335 PO4.11: 8 residues within 4Å: Chain B: N.112, G.113, K.114, T.115, S.116, R.335, Y.351 Ligands: MG.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.113, B:K.114, B:T.115, B:S.116 Water bridges: B:S.116 Salt bridges: B:R.335

2 x K: POTASSIUM ION(Non-covalent)

K.6: 5 residues within 4Å: Chain A: S.100, L.103, T.105, E.192, D.194 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:S.100, A:L.103, A:T.105, A:D.194 K.12: 5 residues within 4Å: Chain B: S.100, L.103, T.105, E.192, D.194 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:S.100, B:L.103, B:T.105, B:D.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L. et al., Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy. Nat.Chem.Biol. (2021)

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

Related Entries With Identical Sequence