SMTL ID : 6os5.2 (2 other biounits)

Crystal structure of CymD prenyltransferase complexed with L-tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 13 residues within 4Å: Chain A: D.57, V.58, E.66, M.134, F.194, L.195, Y.211, R.213, V.257, Y.276, Y.328, Y.343 Ligands: IMD.3 15 PLIP interactions: 12 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.276 Hydrogen bonds: A:D.57, A:E.66, A:Y.328, W.1, W.1 Water bridges: A:R.213, A:R.213, A:R.213, A:R.213, A:R.213, A:N.327, W.1 Salt bridges: A:R.213 pi-Stacking: A:Y.328

1 x DPO: DIPHOSPHATE(Non-covalent)

DPO.2: 11 residues within 4Å: Chain A: Q.79, K.148, W.150, R.207, K.209, Y.211, Y.276, R.339, K.341, Y.343 Ligands: IMD.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Q.79, A:Y.343 Water bridges: A:R.207, A:R.207, A:R.207, A:K.209, A:Y.276, A:R.339, A:R.339, A:R.339 Salt bridges: A:K.148, A:K.148, A:R.207, A:K.209, A:K.209, A:R.339, A:K.341, A:K.341

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 11 residues within 4Å: Chain A: E.66, Q.79, A.81, M.134, W.150, L.195, Y.211, Y.276, Y.343 Ligands: TRP.1, DPO.2 3 PLIP interactions: 1 Ligand-Ligand interactions, 2 interactions with chain A pi-Stacking: W.1, A:W.150, A:W.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roose, B.W. et al., Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD. Biochemistry (2019)

Release Date

2019-07-17

Peptides

CymD prenyltransferase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

CymD prenyltransferase

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