SMTL ID : 3rul.1 (3 other biounits)

New strategy to analyze structures of glycopeptide-target complexes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x HGM- DTY- HCL- GHP- GHP- OMY- HG7: Dalbavancin(Non-covalent)

HGM-DTY-HCL-GHP-GHP-OMY-HG7.1: 7 residues within 4Å: Chain A: G.75, K.77, A.78, A.79 Ligands: N1L.4, MAN.5, M12.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.77 Hydrogen bonds: A:K.77, A:K.77, A:K.77

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.2: 3 residues within 4Å: Chain A: R.42, Q.49, R.72 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.49, A:R.72 Salt bridges: A:R.42, A:R.72 TLA.3: 2 residues within 4Å: Chain A: T.9, K.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.9 Salt bridges: A:K.11

1 x N1L: 2-amino-2-deoxy-beta-D-glucopyranuronic acid(Non-covalent)

N1L.4: 5 residues within 4Å: Chain A: A.79 Ligands: HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, M12.6 No protein-ligand interaction detected (PLIP)

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.5: 5 residues within 4Å: Chain A: A.78 Ligands: HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1 No protein-ligand interaction detected (PLIP)

1 x M12: 10-METHYLUNDECANOIC ACID(Non-functional Binders)

M12.6: 4 residues within 4Å: Ligands: HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, HGM-DTY-HCL-GHP-GHP-OMY-HG7.1, N1L.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Economou, N.J. et al., A carrier protein strategy yields the structure of dalbavancin. J.Am.Chem.Soc. (2012)

Release Date

2012-06-06

Peptides

Ubiquitin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ubiquitin

Related Entries With Identical Sequence