SMTL ID : 1rrv.1 (1 other biounit)

X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MLU-OMZ-ASN-GHP-GHP-OMY-3FG.1: 25 residues within 4Å: Chain A: C.8, G.9, T.10, L.55, M.59, M.60, L.61, Q.62, E.63, M.65, P.66, P.67, P.68, E.73, L.76, A.77, T.80, D.103, D.141, P.143, R.165, Y.166, N.331, T.332 Ligands: BGC.6 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.55, A:L.61, A:L.61, A:P.67, A:E.73, A:D.141, A:N.331, A:T.332 Hydrogen bonds: A:L.61, A:T.80, A:T.80 Water bridges: A:T.10, A:T.10, A:L.61, A:E.63, A:E.63, A:N.331, A:N.331

1 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: S.311, T.332, D.333 Ligands: GOL.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.311, A:T.332, A:D.333, H2O.5, H2O.11

1 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.3: 18 residues within 4Å: Chain A: T.10, R.11, G.12, E.15, L.218, R.223, G.245, S.246, E.293, V.294, F.296, H.309, S.311, A.312, G.313, T.314, V.317 Ligands: GOL.5 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.296 Hydrogen bonds: A:T.10, A:T.10, A:G.12, A:R.223, A:S.246, A:S.246, A:V.294, A:V.294, A:F.296, A:S.311, A:S.311, A:G.313, A:T.314 Water bridges: A:S.246 Salt bridges: A:H.309, A:H.309 pi-Stacking: A:F.296

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: H.58, M.60, Q.62, M.65, W.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.60, A:Q.62 Water bridges: A:W.276 GOL.5: 10 residues within 4Å: Chain A: T.10, G.12, D.13, P.126, S.311, A.312, D.333 Ligands: K.2, TYD.3, BGC.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.13, A:A.312 Water bridges: A:T.10, A:T.10

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

BGC.6: 8 residues within 4Å: Chain A: T.10, D.13, G.102, D.103 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, GOL.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.10, A:D.13, A:D.13 Water bridges: A:T.10, A:G.102, A:D.103, A:L.104, A:L.104, A:L.104, A:Y.123, A:Y.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mulichak, A.M. et al., Crystal Structure of Vancosaminyltransferase Gtfd from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands. Biochemistry (2004)

Release Date

2004-05-18

Peptides

GLYCOSYLTRANSFERASE GTFD: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

GLYCOSYLTRANSFERASE GTFD

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