SMTL ID : 7z6k.1

CRYSTAL STRUCTURE OF WEISSELLA VIRIDESCENS FEMXVV NON-RIBOSOMAL AMINO ACID TRANSFERASE IN COMPLEX WITH A PEPTIDYL-XNA CONJUGATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x A5L- CFL- CFL- A9Z: 2'F-ANA (5'-D(P*(A5L)P*(CFL)P*(CFL))-R(P*(A9Z))-3')(Non-covalent)

A5L-CFL-CFL-A9Z.1: 14 residues within 4Å: Chain A: M.203, R.206, H.207, Y.255, A.258, G.259, S.260, P.269, Y.270, S.301, L.302, F.305, K.306 Ligands: ALA-FGA-CYS-DAL-DAL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.258, A:A.258, A:G.259, A:S.301, A:S.301, A:K.306 Water bridges: A:Y.255, A:S.260, A:S.260, A:R.206 Salt bridges: A:R.206, A:H.207

1 x ALA- FGA- CYS- DAL- DAL: UDP-MurNAc-pentapeptide(Non-covalent)

ALA-FGA-CYS-DAL-DAL.2: 16 residues within 4Å: Chain A: W.33, K.37, M.139, H.140, I.143, Q.144, P.145, I.209, T.210, R.212, Y.216, W.254, Y.257 Ligands: A5L-CFL-CFL-A9Z.1, UDP.4, MUB.5 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.33, A:I.209, A:W.254 Hydrogen bonds: A:Q.144, A:Q.144, A:T.210, A:T.210, A:T.210, A:R.212, A:Y.257 Water bridges: A:W.33, A:K.37, A:K.37 Salt bridges: A:K.37, A:R.212

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: I.214, E.215 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.215, A:E.215

1 x UDP: URIDINE-5'-DIPHOSPHATE(Non-covalent)

UDP.4: 11 residues within 4Å: Chain A: K.37, N.39, W.40, T.65, F.71, Y.104, R.107, I.143, R.212 Ligands: ALA-FGA-CYS-DAL-DAL.2, MUB.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.71 Hydrogen bonds: A:N.39, A:W.40, A:Y.104, A:Y.104, A:R.107 Water bridges: A:K.37, A:K.37, A:R.107 Salt bridges: A:K.37, A:K.37, A:R.212, A:R.212 pi-Stacking: A:F.71

1 x MUB: N-acetyl-alpha-muramic acid(Non-covalent)

MUB.5: 9 residues within 4Å: Chain A: N.39, T.210, H.211, R.212 Ligands: ALA-FGA-CYS-DAL-DAL.2, ALA-FGA-CYS-DAL-DAL.2, ALA-FGA-CYS-DAL-DAL.2, ALA-FGA-CYS-DAL-DAL.2, UDP.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.212 Hydrogen bonds: A:N.39, A:R.212 Water bridges: A:R.212 Salt bridges: A:R.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rietmeyer, L. et al., Amino-acyl tXNA as inhibitors or amino acid donors in peptide synthesis. Nucleic Acids Res. (2022)

Release Date

2022-10-26

Peptides

UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

UDP-N-acetylmuramoylpentapeptide-lysine N(6)-alanyltransferase

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