SMTL ID : 5jr3.2 (1 other biounit)

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 17 residues within 4Å: Chain A: Y.163, R.173, L.180, F.188, G.207, G.208, G.209, E.230, M.231, G.256, D.257, F.258, F.259, S.272, F.273, N.277, W.278 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:D.257, A:D.257, A:F.258, A:S.272 Water bridges: A:L.180, A:S.272, A:S.272, A:S.272 pi-Stacking: A:Y.163, A:F.258 SAH.9: 17 residues within 4Å: Chain B: Y.163, R.173, L.180, F.188, G.207, G.208, G.209, E.230, M.231, G.256, D.257, F.258, F.259, S.272, F.273, N.277, W.278 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:R.173, B:R.173, B:G.207, B:D.257, B:D.257, B:F.258, B:S.272 Water bridges: B:D.177, B:S.272, B:S.272, B:S.272 pi-Stacking: B:Y.163, B:F.258

2 x 4MU: 7-hydroxy-4-methyl-2H-chromen-2-one(Non-covalent)

4MU.2: 8 residues within 4Å: Chain A: W.126, F.176, F.273, E.319, L.320, R.323, M.324, Y.362 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.273, A:F.273, A:L.320 Water bridges: A:N.277, A:L.320 Salt bridges: A:R.323 pi-Stacking: A:W.126 4MU.10: 6 residues within 4Å: Chain B: F.176, L.180, E.319, L.320, R.323, M.324 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.180, B:L.180, B:L.320 Hydrogen bonds: B:E.319 Water bridges: B:N.277, B:N.277 Salt bridges: B:R.323 pi-Stacking: B:W.126

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

SO4.3: 1 residues within 4Å: Chain A: R.148 No protein-ligand interaction detected (PLIP) SO4.4: 2 residues within 4Å: Chain A: R.135, R.169 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.135, A:R.169 SO4.5: 3 residues within 4Å: Chain A: R.81, P.82, E.83 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.83 Water bridges: A:R.81 Salt bridges: A:R.81 SO4.6: 4 residues within 4Å: Chain A: R.151, P.279, H.281 Chain B: R.81 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Salt bridges: B:R.81, A:R.151, A:H.281 Water bridges: A:D.280 SO4.7: 6 residues within 4Å: Chain A: H.309, T.334, K.337 Chain B: E.83, L.86, R.90 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Water bridges: B:R.90, B:R.90, A:T.334 Salt bridges: B:R.90, A:H.309, A:K.337 SO4.8: 3 residues within 4Å: Chain A: R.239, D.252, V.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.253 Salt bridges: A:R.239 SO4.11: 2 residues within 4Å: Chain B: R.135, R.169 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.135 Salt bridges: B:R.135, B:R.169 SO4.12: 3 residues within 4Å: Chain B: H.63, A.66, R.77 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.63 Salt bridges: B:H.63, B:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone (to be published). To Be Published

Release Date

2016-06-01

Peptides

Carminomycin 4-O-methyltransferase DnrK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Carminomycin 4-O-methyltransferase DnrK

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