SMTL ID : 4ii9.1

Crystal structure of Weissella viridescens FemXVv non-ribosomal amino acid transferase in complex with a peptidyl-RNA conjugate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x ALA- FGA- CYS- DAL- DAL: 5-mer peptide(Non-covalent)

ALA-FGA-CYS-DAL-DAL.1: 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: C-C-A9Z.2, UDP.4, MUB.5 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.33, 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 Salt bridges: A:K.37, A:R.212

1 x C- C- A9Z: RNA (5'-R(P*CP*CP*(A9Z))-3')(Non-covalent)

C-C-A9Z.2: 17 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, F.305, K.306 Ligands: ALA-FGA-CYS-DAL-DAL.1, ALA-FGA-CYS-DAL-DAL.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.206, A:A.258, A:A.258, A:S.260, A:K.306 Salt bridges: A:H.207

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.81 Water bridges: A:I.54

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.1, 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: N.39, T.210, H.211, R.212 Ligands: ALA-FGA-CYS-DAL-DAL.1, ALA-FGA-CYS-DAL-DAL.1, ALA-FGA-CYS-DAL-DAL.1, UDP.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:R.212 Water bridges: A:N.39, A:N.39, A:N.39, A:N.39, A:H.211, A:R.212, A:R.212 Salt bridges: A:R.212

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fonvielle, M. et al., The Structure of FemXWv in Complex with a Peptidyl-RNA Conjugate: Mechanism of Aminoacyl Transfer from Ala-tRNA(Ala) to Peptidoglycan Precursors. Angew.Chem.Int.Ed.Engl. (2013)

Release Date

2013-07-03

Peptides

FemX: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

FemX

Related Entries With Identical Sequence