SMTL ID : 6m83.1

Crystal structure of TylM1 S120A bound to SAH and dTDP-phenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 19 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, A.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: 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, A.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: 17 residues within 4Å: Chain A: Y.14, 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 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.152, A:Y.162, A:Y.162, A:I.190 Hydrogen bonds: A:N.157, A:T.159, A:T.159, A:S.179, A:S.181, A:S.181 Water bridges: A:R.177, A:R.241, A:R.241, A:R.241 Salt bridges: A:K.29, A:K.29, A:R.177, A:R.177, A:R.241 pi-Stacking: A:W.153 TLO.5: 17 residues within 4Å: Chain B: Y.14, 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 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:W.152, B:Y.162, B:Y.162, B:I.190 Hydrogen bonds: B:N.157, B:T.159, B:T.159, B:S.179, B:S.181, B:S.181 Water bridges: B:R.177, B:R.241, B:R.241, B:R.241 Salt bridges: B:K.29, B:K.29, B:R.177, B:R.177, B:R.241 pi-Stacking: B:W.153

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: G.198, P.199, D.200, R.201 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: G.198, P.199, D.200, R.201 Ligand excluded by PLIP

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