SMTL ID : 4hh4.1

Structure of the CcbJ Methyltransferase from Streptomyces caelestis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-hexamer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: E.26, Y.29, G.30, Y.37, E.68, G.70, V.71, G.72, R.75, E.91, S.92, S.93, M.96, G.118, N.119, F.120, F.137, T.139, C.142, L.143 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.30, A:Y.37, A:G.70, A:S.92, A:N.119, A:F.120 Water bridges: A:V.76 Salt bridges: A:R.75 SAH.7: 21 residues within 4Å: Chain B: E.26, Y.29, G.30, Y.37, E.68, G.70, V.71, G.72, R.75, E.91, S.92, S.93, M.96, G.118, N.119, F.120, F.137, T.139, C.142, L.143 Ligands: GOL.10 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.30, B:Y.37, B:G.70, B:S.92, B:N.119, B:F.120 Water bridges: B:T.139 Salt bridges: B:R.75 pi-Stacking: B:F.120 SAH.12: 20 residues within 4Å: Chain C: E.26, Y.29, G.30, Y.37, E.68, G.70, V.71, G.72, R.75, E.91, S.92, S.93, M.96, G.118, N.119, F.120, F.137, T.139, C.142, L.143 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.30, C:G.70, C:S.92, C:N.119, C:F.120 Water bridges: C:V.71, C:R.75 Salt bridges: C:R.75 pi-Stacking: C:F.120 SAH.18: 19 residues within 4Å: Chain D: E.26, Y.29, G.30, Y.37, E.68, G.70, V.71, G.72, R.75, E.91, S.92, S.93, M.96, G.118, N.119, F.120, T.139, C.142, L.143 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.30, D:Y.37, D:G.70, D:S.92, D:N.119, D:F.120 Water bridges: D:R.75 Salt bridges: D:R.75 SAH.22: 19 residues within 4Å: Chain E: E.26, Y.29, G.30, Y.37, E.68, G.70, V.71, G.72, R.75, E.91, S.92, S.93, M.96, G.118, N.119, F.120, T.139, C.142, L.143 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:G.30, E:Y.37, E:E.68, E:G.70, E:S.92, E:N.119, E:F.120 Water bridges: E:R.75 Salt bridges: E:R.75 pi-Stacking: E:F.120 SAH.30: 20 residues within 4Å: Chain F: E.26, Y.29, G.30, Y.37, E.68, G.70, V.71, G.72, R.75, E.91, S.92, S.93, M.96, G.118, N.119, F.120, F.137, T.139, C.142, L.143 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.30, F:G.70, F:S.92, F:N.119, F:F.120 Salt bridges: F:R.75

20 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: S.262, S.263, R.264, Y.265 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: R.51 Ligand excluded by PLIP SO4.4: 3 residues within 4Å: Chain A: R.250, F.259 Chain F: L.204 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain B: S.263, R.264 Ligand excluded by PLIP SO4.9: 1 residues within 4Å: Chain B: R.129 Ligand excluded by PLIP SO4.13: 2 residues within 4Å: Chain C: G.118, N.119 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain C: R.257 Chain F: R.257, R.258 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain C: S.263, R.264, Y.265 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain C: R.129, E.158 Ligand excluded by PLIP SO4.19: 4 residues within 4Å: Chain D: A.252, S.262, S.263, R.264 Ligand excluded by PLIP SO4.20: 1 residues within 4Å: Chain D: R.129 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain A: R.257 Chain E: R.257, R.258 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain A: R.257, R.258 Chain E: R.257 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain E: D.253, S.263, R.264, Y.265 Ligand excluded by PLIP SO4.26: 1 residues within 4Å: Chain E: R.129 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain E: R.64, P.65, Q.128 Ligand excluded by PLIP SO4.28: 3 residues within 4Å: Chain B: L.204 Chain E: R.250, F.259 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain C: R.257, R.258 Chain F: R.257 Ligand excluded by PLIP SO4.32: 3 residues within 4Å: Chain F: S.263, R.264, Y.265 Ligand excluded by PLIP SO4.33: 1 residues within 4Å: Chain F: R.129 Ligand excluded by PLIP

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: Y.29, F.137, N.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.29, A:N.138 Water bridges: A:Y.29, A:Y.29 GOL.6: 1 residues within 4Å: Chain A: R.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.256 GOL.10: 4 residues within 4Å: Chain B: Y.29, F.137, N.138 Ligands: SAH.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.137, B:N.138 GOL.17: 5 residues within 4Å: Chain C: Y.29, F.137, N.138, Y.226, L.228 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.29, C:Y.29, C:N.138 GOL.21: 4 residues within 4Å: Chain D: Y.29, F.137, N.138, Y.226 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.137 GOL.29: 1 residues within 4Å: Chain E: F.137 No protein-ligand interaction detected (PLIP)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 4 residues within 4Å: Chain B: R.257, R.258 Chain D: R.257, R.258 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:R.258, D:R.257, D:R.258 Salt bridges: B:R.257, D:R.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bauer, J. et al., Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis. Acta Crystallogr.,Sect.D (2014)

Release Date

2013-10-30

Peptides

CcbJ: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

CcbJ

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