SMTL ID : 5bsz.1

X-ray structure of the sugar N-methyltransferase KedS8 from Streptoalloteichus sp ATCC 53650

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SAH.1: 19 residues within 4Å: Chain A: L.15, G.16, L.21, A.55, C.56, G.57, H.61, E.76, L.77, S.78, M.81, A.97, D.98, M.99, F.100, L.114, T.115, S.117, Y.120 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.16, A:A.55, A:L.77, A:S.78, A:D.98, A:D.98, A:M.99, A:S.117 Water bridges: A:C.56, A:H.61, A:H.61, A:L.114 Salt bridges: A:K.28, A:H.61 pi-Stacking: A:Y.120 SAH.7: 19 residues within 4Å: Chain B: L.15, G.16, L.21, A.55, C.56, G.57, H.61, E.76, L.77, S.78, M.81, A.97, D.98, M.99, F.100, L.114, T.115, S.117, Y.120 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.16, B:A.55, B:L.77, B:S.78, B:D.98, B:D.98, B:M.99, B:S.117 Water bridges: B:C.56, B:H.61, B:H.61, B:L.114 Salt bridges: B:K.28, B:H.61 pi-Stacking: B:Y.120 SAH.13: 19 residues within 4Å: Chain C: L.15, G.16, L.21, A.55, C.56, G.57, H.61, E.76, L.77, S.78, M.81, A.97, D.98, M.99, F.100, L.114, T.115, S.117, Y.120 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.16, C:A.55, C:L.77, C:S.78, C:D.98, C:M.99, C:T.115, C:S.117 Water bridges: C:C.56, C:L.114 Salt bridges: C:K.28, C:H.61 pi-Stacking: C:Y.120 SAH.19: 19 residues within 4Å: Chain D: L.15, G.16, L.21, A.55, C.56, G.57, H.61, E.76, L.77, S.78, M.81, A.97, D.98, M.99, F.100, L.114, T.115, S.117, Y.120 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:G.16, D:A.55, D:L.77, D:S.78, D:D.98, D:M.99, D:T.115, D:S.117 Water bridges: D:C.56, D:L.114 Salt bridges: D:K.28, D:H.61 pi-Stacking: D:Y.120

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

EDO.2: 4 residues within 4Å: Chain A: D.207 Chain B: D.207 Chain D: M.3 Ligands: EDO.8 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: E.86, R.87, L.89, A.91 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: H.95, D.103 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain B: S.7 Chain C: S.203, V.205 Chain D: Y.11 Ligands: EDO.11 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: D.207 Chain B: D.207 Chain C: M.3 Ligands: EDO.2 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain B: E.86, R.87, L.89, A.91 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain B: H.95, D.103 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: S.7 Chain C: Y.11 Chain D: S.203, V.205 Ligands: EDO.5 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain B: M.3 Chain C: D.207 Chain D: D.207 Ligands: EDO.20 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: E.86, R.87, L.89, A.91 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain C: H.95, D.103 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: S.203, V.205 Chain B: Y.11 Chain D: S.7 Ligands: EDO.23 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: M.3 Chain C: D.207 Chain D: D.207 Ligands: EDO.14 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain D: E.86, R.87, L.89, A.91 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain D: H.95, D.103 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: Y.11 Chain B: S.203, V.205 Chain C: S.7 Ligands: EDO.17 Ligand excluded by PLIP

4 x THM: THYMIDINE(Non-covalent)

THM.6: 8 residues within 4Å: Chain A: W.150, T.154, F.155, L.156, H.159, S.178, H.187, R.237 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.150, A:L.156, A:H.159 Hydrogen bonds: A:T.154, A:L.156, A:S.178, A:R.237 pi-Stacking: A:W.150, A:W.150 THM.12: 8 residues within 4Å: Chain B: W.150, T.154, F.155, L.156, H.159, S.178, H.187, R.237 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.150, B:L.156, B:H.159 Hydrogen bonds: B:T.154, B:L.156, B:S.178, B:R.237 pi-Stacking: B:W.150, B:W.150 THM.18: 8 residues within 4Å: Chain C: W.150, T.154, F.155, L.156, H.159, S.178, H.187, R.237 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.150, C:L.156, C:H.159 Hydrogen bonds: C:T.154, C:L.156, C:S.178, C:H.187, C:R.237 pi-Stacking: C:W.150, C:W.150 THM.24: 8 residues within 4Å: Chain D: W.150, T.154, F.155, L.156, H.159, S.178, H.187, R.237 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.150, D:L.156, D:H.159 Hydrogen bonds: D:T.154, D:L.156, D:S.178, D:H.187, D:R.237 pi-Stacking: D:W.150, D:W.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delvaux, N.A. et al., Molecular architecture of KedS8, a sugar N-methyltransferase from Streptoalloteichus sp. ATCC 53650. Protein Sci. (2015)

Release Date

2015-07-29

Peptides

N-methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

N-methyltransferase