SMTL ID : 3pfh.1

X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in complex with SAH and dTDP-Quip3N

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 20 residues within 4Å: Chain A: Y.14, Y.22, Y.33, A.58, C.59, G.60, H.64, E.79, L.80, S.81, M.84, G.100, D.101, M.102, R.103, M.117, F.118, S.120, H.123 Ligands: T3Q.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.22, A:A.58, A:L.80, A:D.101, A:D.101, A:M.102, A:S.120 Water bridges: A:Y.33, A:M.63, A:M.117 Salt bridges: A:H.64 SAH.4: 20 residues within 4Å: Chain B: Y.14, Y.22, Y.33, A.58, C.59, G.60, H.64, E.79, L.80, S.81, M.84, G.100, D.101, M.102, R.103, M.117, F.118, S.120, H.123 Ligands: T3Q.5 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.33, B:A.58, B:L.80, B:D.101, B:M.102, B:R.103, B:S.120 Water bridges: B:Y.33, B:C.59, B:G.62, B:M.117 Salt bridges: B:H.64

2 x T3Q: [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate(Non-covalent)

T3Q.2: 17 residues within 4Å: Chain A: Y.14, H.26, K.29, F.118, W.152, W.153, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, H.210, R.241 Ligands: SAH.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:W.153, A:Y.162, A:Y.162 Hydrogen bonds: A:Y.14, A:Y.14, A:F.118, A:T.159, A:S.179, A:S.179, A:S.181, A:S.181, A:R.241, A:R.241 Water bridges: A:Y.14, A:H.26, A:K.29, A:K.29, A:S.119, A:Y.162 Salt bridges: A:H.26, A:K.29, A:K.29, A:R.177, A:R.177, A:R.177, A:R.241 pi-Stacking: A:Y.162 T3Q.5: 18 residues within 4Å: Chain B: Y.14, H.26, K.29, F.118, W.152, W.153, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, T.188, I.190, H.210, R.241 Ligands: SAH.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:Y.162, B:Y.162 Hydrogen bonds: B:Y.14, B:F.118, B:T.159, B:S.179, B:S.179, B:S.181, B:S.181, B:R.241, B:R.241 Water bridges: B:Y.14, B:K.29, B:K.29, B:F.118, B:T.159, B:T.159 Salt bridges: B:H.26, B:K.29, B:K.29, B:R.177, B:R.177, B:R.177, B:R.241 pi-Stacking: B:W.153, B:Y.162

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: G.126, Q.127, E.186, T.213, L.214, F.215, Q.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.127, A:E.186, A:L.214, A:Q.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carney, A.E. et al., Molecular Architecture of TylM1 from Streptomyces fradiae: An N,N-Dimethyltransferase Involved in the Production of dTDP-d-mycaminose . Biochemistry (2011)

Release Date

2010-12-15

Peptides

N-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

N-methyltransferase

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