SMTL ID : 3vfj.1

The structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a ligand carrier

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x GHP- 3MY- 3FG- GHP- GHP- OMX- 3FG: MonodeChloro- Teicoplanin A2-2(Non-covalent)

GHP-3MY-3FG-GHP-GHP-OMX-3FG.1: 10 residues within 4Å: Chain A: C.375, K.376, A.377, A.378 Ligands: CAC.12, GCS.13, T55.14, NAG.15, MAN.16, CAC.17 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.376, A:K.376 Hydrogen bonds: A:K.376

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: E.112 Ligands: ACT.11 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.112, A:E.112 ZN.3: 1 residues within 4Å: Chain A: D.66 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, A:D.66, H2O.2 ZN.4: 2 residues within 4Å: Chain A: E.289, E.292 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.289, A:E.289, A:E.292, A:E.292 ZN.5: 2 residues within 4Å: Chain A: E.360, D.364 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.360, A:D.364, A:D.364, H2O.5 ZN.6: 2 residues within 4Å: Chain A: E.173, D.178 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.173, A:D.178, H2O.5 ZN.7: 3 residues within 4Å: Chain A: P.134, N.202, H.204 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.204, H2O.2, H2O.2, H2O.5, H2O.5 ZN.8: 1 residues within 4Å: Chain A: H.40 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.40, A:H.40, H2O.4 ZN.9: 1 residues within 4Å: Chain A: D.83 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.83

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 3 residues within 4Å: Chain A: K.27, E.289, A.293 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.293 ACT.11: 6 residues within 4Å: Chain A: K.16, A.64, E.112, G.261, L.263 Ligands: ZN.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.263 Water bridges: A:K.16, A:K.16, A:L.263 Salt bridges: A:K.16

2 x CAC: CACODYLATE ION(Non-covalent)(Non-functional Binders)

CAC.12: 3 residues within 4Å: Chain A: C.375 Ligands: GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, CAC.17 No protein-ligand interaction detected (PLIP) CAC.17: 4 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, CAC.12, T55.14 No protein-ligand interaction detected (PLIP)

1 x GCS: 2-amino-2-deoxy-beta-D-glucopyranose(Non-covalent)

GCS.13: 5 residues within 4Å: Chain A: A.378 Ligands: GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, T55.14 No protein-ligand interaction detected (PLIP)

1 x T55: 8-METHYLNONANOIC ACID(Non-functional Binders)

T55.14: 5 residues within 4Å: Ligands: GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GCS.13, CAC.17 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.15: 3 residues within 4Å: Chain A: G.374 Ligands: GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1 No protein-ligand interaction detected (PLIP)

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

MAN.16: 6 residues within 4Å: Chain A: Q.73, S.74, A.377 Ligands: GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1, GHP-3MY-3FG-GHP-GHP-OMX-3FG.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Economou, N.J. et al., Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-01-09

Peptides

Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Maltose-binding periplasmic protein, C-terminal fused by Cys-Lys-D-Ala-D-Ala

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