SMTL ID : 9gdj.1 (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

1 x NCO: COBALT HEXAMMINE(III)(Non-covalent)

NCO.1: 3 residues within 4Å: Chain A: E.256, L.290, E.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.291, A:E.291

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

PGE.2: 5 residues within 4Å: Chain A: S.148, E.149, P.211, Y.243, P.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.149 Water bridges: A:S.150, A:P.211 PGE.3: 3 residues within 4Å: Chain A: A.87, R.112, M.113 No protein-ligand interaction detected (PLIP) PGE.4: 4 residues within 4Å: Chain A: Q.66, Q.68, D.69, P.71 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.66, A:D.69

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: Q.176, Y.179, P.244, L.245, P.246, H.247, D.280 Ligands: IPA.14 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: E.51, S.52, R.54, V.57, A.141, D.172, N.267, Y.268, Y.279 Ligand excluded by PLIP GOL.7: 7 residues within 4Å: Chain A: V.95, V.96, T.97, K.116, T.117, T.118 Ligands: IPA.15 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: 6 residues within 4Å: Chain A: I.127, A.129, A.131, A.158, R.161, L.162 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: A.103, L.106, E.107, R.121 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: D.47, Q.48 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: H.247, A.262, R.263, A.264, W.282 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: R.70, G.132, E.133, D.135 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain B: F.174, G.175, Q.176, Y.179, P.244, L.245, P.246, H.247, D.280 Ligand excluded by PLIP GOL.20: 9 residues within 4Å: Chain B: E.51, S.52, R.54, A.141, G.142, D.172, N.267, Y.268, Y.279 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: V.95, V.96, T.97, K.116, T.117, T.118 Ligands: IPA.26 Ligand excluded by PLIP GOL.22: 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.23: 5 residues within 4Å: Chain B: I.127, A.129, A.158, R.161, L.162 Ligand excluded by PLIP GOL.24: 4 residues within 4Å: Chain B: L.106, E.107, R.110, L.119 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: Q.62, V.72, R.73, R.92, G.93, Y.94 Ligand excluded by PLIP

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

IPA.14: 4 residues within 4Å: Chain A: K.206, V.213, P.244 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.213, A:P.244, A:P.244 Hydrogen bonds: A:K.206, A:K.206 IPA.15: 6 residues within 4Å: Chain A: A.90, Y.94, V.95, V.96, T.117 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.96, A:T.117 Hydrogen bonds: A:Y.94, A:V.96 IPA.16: 4 residues within 4Å: Chain A: Q.49, F.182, W.202, M.215 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.182, A:W.202 Hydrogen bonds: A:Q.49 IPA.26: 7 residues within 4Å: Chain B: A.90, Y.94, V.95, V.96, M.113, T.117 Ligands: GOL.21 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.90 Hydrogen bonds: B:V.96 Water bridges: B:A.90

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

SAH.17: 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 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Y.38, A:C.79, A:G.81, A:M.85, A:R.101, A:R.101, A:E.123, A:L.124, A:L.124 Water bridges: A:G.83, A:G.83, A:G.142 Salt bridges: A:R.54 pi-Cation interactions: A:R.101 SAH.27: 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 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:Y.38, B:Y.38, B:C.79, B:G.81, B:R.101, B:R.101, B:E.123, B:L.124, B:L.124 Water bridges: B:M.85 Salt bridges: B:R.54 pi-Cation interactions: B:R.101

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

CL.18: 3 residues within 4Å: Chain B: Q.50, R.56, N.267 Ligand excluded by PLIP

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
A

B
B

Methyltransferase

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