SMTL ID : 9gdj.2 (1 other biounit)

C-Methyltransferase SgMT from Streptomyces griseoviridis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: Q.62, R.91, R.92 Ligand excluded by PLIP GOL.5: 8 residues within 4Å: Chain A: F.174, Q.176, Y.179, P.244, L.245, P.246, H.247, D.280 Ligand excluded by PLIP GOL.6: 10 residues within 4Å: Chain A: E.51, S.52, R.54, V.57, A.141, D.172, N.267, Y.268, Y.279 Ligands: GOL.13 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: V.96, T.97, K.116, T.117, T.118 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: D.266, D.271, P.272, G.274, P.275, H.276, T.277 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: I.127, A.158, R.161, L.162 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: Q.62, V.72, R.92, G.93, Y.94 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: D.261, A.262, R.263 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: S.224, R.225, E.230, P.231, A.232 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: A.141, G.142, F.174, Y.217, Y.242, Y.279 Ligands: GOL.6, IPA.17 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain A: E.149, S.150, S.153, R.252, L.253, E.256 Ligand excluded by PLIP GOL.15: 1 residues within 4Å: Chain A: L.239 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: Q.62, R.91, R.92 Ligand excluded by PLIP GOL.23: 8 residues within 4Å: Chain B: F.174, Q.176, Y.179, P.244, L.245, P.246, H.247, D.280 Ligand excluded by PLIP GOL.24: 10 residues within 4Å: Chain B: E.51, S.52, R.54, V.57, A.141, D.172, N.267, Y.268, Y.279 Ligands: GOL.31 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain B: V.96, T.97, K.116, T.117, T.118 Ligand excluded by PLIP GOL.26: 7 residues within 4Å: Chain B: D.266, D.271, P.272, G.274, P.275, H.276, T.277 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: I.127, A.158, R.161, L.162 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: Q.62, V.72, R.92, G.93, Y.94 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: D.261, A.262, R.263 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: S.224, R.225, E.230, P.231, A.232 Ligand excluded by PLIP GOL.31: 8 residues within 4Å: Chain B: A.141, G.142, F.174, Y.217, Y.242, Y.279 Ligands: GOL.24, IPA.35 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain B: E.149, S.150, S.153, R.252, L.253, E.256 Ligand excluded by PLIP GOL.33: 1 residues within 4Å: Chain B: L.239 Ligand excluded by PLIP

6 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 1 residues within 4Å: Chain A: D.47 No protein-ligand interaction detected (PLIP) IPA.16: 5 residues within 4Å: Chain A: D.59, Q.62, T.63, Q.66, R.92 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.62 Hydrogen bonds: A:D.59, A:R.92 IPA.17: 5 residues within 4Å: Chain A: Q.50, E.51, W.202, Y.217 Ligands: GOL.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.202 Hydrogen bonds: A:Q.50 IPA.20: 1 residues within 4Å: Chain B: D.47 No protein-ligand interaction detected (PLIP) IPA.34: 5 residues within 4Å: Chain B: D.59, Q.62, T.63, Q.66, R.92 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Q.62 Hydrogen bonds: B:D.59, B:D.59, B:R.92 IPA.35: 5 residues within 4Å: Chain B: Q.50, E.51, W.202, Y.217 Ligands: GOL.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.202 Hydrogen bonds: B:Q.50

4 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: S.148, E.149, P.211, Y.243, P.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.149, A:P.244 Water bridges: A:S.148, A:S.150 PGE.4: 7 residues within 4Å: Chain A: D.184, P.185, S.186, A.187, P.188, T.205, K.206 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.187, A:K.206 PGE.21: 5 residues within 4Å: Chain B: S.148, E.149, P.211, Y.243, P.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.149, B:P.244 Water bridges: B:S.148, B:S.150 PGE.22: 7 residues within 4Å: Chain B: D.184, P.185, S.186, A.187, P.188, T.205, K.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.187, B:K.206

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

SAH.18: 21 residues within 4Å: Chain A: Y.31, Y.38, R.54, E.77, C.79, C.80, G.81, L.84, M.85, D.100, R.101, S.102, M.105, A.122, E.123, L.124, A.140, A.141, G.143, Y.146, L.147 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.38, A:Y.38, A:R.101, A:R.101, A:E.123, A:L.124, A:L.124, A:A.140 Water bridges: A:M.85 Salt bridges: A:R.54 pi-Cation interactions: A:R.101 SAH.36: 21 residues within 4Å: Chain B: Y.31, Y.38, R.54, E.77, C.79, C.80, G.81, L.84, M.85, D.100, R.101, S.102, M.105, A.122, E.123, L.124, A.140, A.141, G.143, Y.146, L.147 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.38, B:R.101, B:R.101, B:L.124, B:L.124, B:A.140 Water bridges: B:M.85 Salt bridges: B:R.54 pi-Cation interactions: B:R.101

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haase, M. et al., Characterization of a C-methyltransferase from Streptomyces griseoviridis - crystal structure, mechanism, and substrate scope. Chem Sci (2025)

Release Date

2025-02-19

Peptides

Methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Methyltransferase

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