SMTL ID : 3run.1

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x MLU- OMZ- ASN- GHP- GHP- OMY- 3FG: VANCOMYCIN(Non-covalent)

MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1: 13 residues within 4Å: Chain A: M.1, E.5, R.8, Y.161, K.162, N.163, C.165, K.166, A.167, A.168 Ligands: BGC-RER.2, BGC-RER.2, MRD.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.166 Hydrogen bonds: A:E.5, A:R.8, A:R.8, A:Y.161, A:N.163, A:K.166 Water bridges: A:M.1, A:M.1, A:R.8, A:K.162, A:K.162

1 x BGC- RER: vancosamine-(1-2)-beta-D-glucopyranose(Non-covalent)

BGC-RER.2: 4 residues within 4Å: Chain A: C.165 Ligands: MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1, MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1, MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1 No protein-ligand interaction detected (PLIP)

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: G.110, G.113, F.114 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.114 Hydrogen bonds: A:G.110

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.4: 2 residues within 4Å: Chain A: V.71, D.72 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.71 Hydrogen bonds: A:D.72 MRD.10: 6 residues within 4Å: Chain A: E.5, R.8, A.167 Ligands: MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1, MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1, MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.5

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

PO4.5: 2 residues within 4Å: Chain A: R.14, K.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.14, A:K.19, A:K.19

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 6 residues within 4Å: Chain A: E.11, D.20, G.30, L.32, F.104, Q.105 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.11, A:L.32, A:Q.105, A:R.145 Water bridges: A:E.11, A:E.11, A:E.11, A:Y.18, A:G.30, A:F.104

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

CL.7: 4 residues within 4Å: Chain A: T.142, P.143, N.144, R.145 Ligand excluded by PLIP

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.8: 2 residues within 4Å: Chain A: Y.139, K.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.147, A:K.147 IPA.9: 0 residues within 4Å: (No contacts) 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

LYSOZYME: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSOZYME