SMTL ID : 6m82.1

Crystal structure of TylM1 Y14paF bound to SAH and dTDP-phenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: X.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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.22, A:Y.33, A:A.58, A:G.60, A:L.80, A:S.81, A:D.101, A:D.101, A:M.102 Water bridges: A:Y.33, A:C.59, A:G.62, A:H.64, A:H.64, A:M.117 Salt bridges: A:H.64 SAH.4: 19 residues within 4Å: Chain B: X.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 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.58, B:G.60, B:L.80, B:S.81, B:D.101, B:M.102 Water bridges: B:Y.33, B:C.59, B:G.62, B:M.117 Salt bridges: B:H.64

2 x TLO: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine(Non-covalent)

TLO.2: 16 residues within 4Å: Chain A: H.26, K.29, F.118, W.152, W.153, N.157, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, H.210, R.241 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.162, A:Y.162, A:I.190 Hydrogen bonds: A:N.157, A:T.159, A:S.179, A:S.181, A:S.181 Water bridges: A:H.26, A:R.241 Salt bridges: A:H.26, A:K.29, A:K.29, A:R.177, A:R.177, A:R.241 pi-Stacking: A:W.153 TLO.5: 16 residues within 4Å: Chain B: H.26, K.29, F.118, W.152, W.153, N.157, F.158, T.159, Y.162, A.164, R.177, S.179, S.181, I.190, H.210, R.241 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.162, B:Y.162, B:I.190 Hydrogen bonds: B:N.157, B:T.159, B:S.179, B:S.181, B:S.181 Water bridges: B:R.241 Salt bridges: B:H.26, B:K.29, B:K.29, B:R.177, B:R.177, B:R.241 pi-Stacking: B:W.153

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

EDO.3: 5 residues within 4Å: Chain A: S.48, P.49, K.50, A.51, D.144 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.48, A:K.50, A:K.50 Water bridges: A:D.144, A:D.144 EDO.6: 5 residues within 4Å: Chain B: S.48, P.49, K.50, A.51, D.144 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.48, B:K.50, B:K.50 Water bridges: B:D.144, B:D.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fick, R.J. et al., Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1. Biochemistry (2019)

Release Date

2019-03-13

Peptides

dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase