SMTL ID : 7z5y.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 1.71 Å

Oligo State

monomer

Ligands

1 x 6HA- 6HC- 6HC- A9Z: HNA (5'-D(P*(6HA)P*(6HC)P*(6HC))-R(P*(A9Z))-3')(Non-covalent)

6HA-6HC-6HC-A9Z.1: 16 residues within 4Å: Chain A: M.203, R.206, H.207, I.209, Y.255, A.258, S.260, G.263, T.265, P.269, G.292, S.301, L.302, K.306 Ligands: ALA-FGA-CYS-DAL-DAL.2, ALA-FGA-CYS-DAL-DAL.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.269 Hydrogen bonds: A:G.263, A:R.206, A:Y.255, A:A.258, A:A.258, A:S.260, A:S.260, A:K.306 Salt bridges: A:H.207, A:H.207

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

ALA-FGA-CYS-DAL-DAL.2: 15 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: 6HA-6HC-6HC-A9Z.1, MUB.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.143, 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, A:H.140, A:I.143 Salt bridges: A:K.37, A:R.212

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.18, I.55, M.80, D.81, L.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.81

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

UDP.4: 10 residues within 4Å: Chain A: K.37, N.39, W.40, T.65, F.71, Y.104, R.107, I.143, R.212 Ligands: 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: 8 residues within 4Å: Chain A: 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.212 Water bridges: A:R.212, 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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