SMTL ID : 3rum.1

New strategy to analyze structures of glycopeptide antibiotic-target complexes

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

2 x GHP- HTY- MP4- GHP- GHP- OMX- MDF: Ristocetin(Non-covalent)

GHP-HTY-MP4-GHP-GHP-OMX-MDF.1: 26 residues within 4Å: Chain A: E.46, P.49, Q.50, G.70, S.74, S.338, Y.342, N.368, A.371, A.373, C.375, K.376, A.377, A.378 Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, BGC-MAN-BXY-RAM.3, BGC-MAN-BXY-RAM.3, BGC-MAN-BXY-RAM.3, BGC-MAN-BXY-RAM.4, BGC-MAN-BXY-RAM.4, RST.12, MAN.13, RST.14 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.49, A:Y.342, A:A.373 Hydrogen bonds: A:Q.50, A:S.74, A:S.74, A:S.338, A:Y.342, A:N.368, A:K.376 Water bridges: A:Q.50, A:A.339 pi-Stacking: A:Y.342 GHP-HTY-MP4-GHP-GHP-OMX-MDF.2: 11 residues within 4Å: Chain A: Q.50 Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, BGC-MAN-BXY-RAM.4, BGC-MAN-BXY-RAM.4, BGC-MAN-BXY-RAM.4, RST.12, RST.14, MAN.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.50

2 x BGC- MAN- BXY- RAM: alpha-D-arabinofuranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-6)]beta-D-glucopyranose(Non-covalent)(Non-functional Binders)

BGC-MAN-BXY-RAM.3: 11 residues within 4Å: Chain A: A.373, G.374, C.375, K.376, A.377 Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, BGC-MAN-BXY-RAM.4, BGC-MAN-BXY-RAM.4, RST.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.374, A:K.376 BGC-MAN-BXY-RAM.4: 10 residues within 4Å: Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, BGC-MAN-BXY-RAM.3, BGC-MAN-BXY-RAM.3, BGC-MAN-BXY-RAM.3, RST.12, SO4.16 No protein-ligand interaction detected (PLIP)

1 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.5: 13 residues within 4Å: Chain A: K.16, W.63, A.64, D.66, R.67, E.112, E.154, P.155, Y.156, F.157, W.231, M.331, W.341 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.63, A:R.67, A:R.67, A:E.154, A:Y.156

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

IPA.6: 2 residues within 4Å: Chain A: M.149, N.206 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.206 Hydrogen bonds: A:N.206 Water bridges: A:T.209 IPA.7: 3 residues within 4Å: Chain A: N.13, D.42, K.43 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.43 Water bridges: A:L.44 IPA.8: 5 residues within 4Å: Chain A: N.151, Q.153, E.154, D.210, Y.211 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.153, A:E.154 Hydrogen bonds: A:N.151, A:Y.211

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain A: S.271, P.272, N.273, K.274, E.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.272, A:K.274, A:E.275 Salt bridges: A:K.274 SO4.10: 3 residues within 4Å: Chain A: P.41, D.42, K.47 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.42 Salt bridges: A:K.47 SO4.11: 4 residues within 4Å: Chain A: K.89, T.287, D.288, E.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.288, A:D.288 Water bridges: A:K.89 Salt bridges: A:K.89 SO4.16: 1 residues within 4Å: Ligands: BGC-MAN-BXY-RAM.4 No protein-ligand interaction detected (PLIP)

2 x RST: 3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose(Non-covalent)(Non-functional Binders)

RST.12: 7 residues within 4Å: Chain A: Q.50, K.376 Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, BGC-MAN-BXY-RAM.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.50 RST.14: 5 residues within 4Å: Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, BGC-MAN-BXY-RAM.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.342

2 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.13: 11 residues within 4Å: Chain A: E.45, E.46, P.49, R.67, Y.71, S.338, A.377 Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1, GHP-HTY-MP4-GHP-GHP-OMX-MDF.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.67, A:R.67, A:S.338, A:S.338 Water bridges: A:R.67 MAN.15: 3 residues within 4Å: Ligands: GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2, GHP-HTY-MP4-GHP-GHP-OMX-MDF.2 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

Maltose-binding periplasmic protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltose-binding periplasmic protein

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