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

Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 2-chloro-4-nitrophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

9 x P9P: 2-chloranyl-4-nitro-phenol(Non-covalent)

P9P.1: 2 residues within 4Å: Chain A: A.193, R.220 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.220 Hydrogen bonds: A:R.220 Water bridges: A:D.189 P9P.3: 14 residues within 4Å: Chain A: W.126, V.133, F.162, Y.163, F.176, L.180, N.277, L.320, R.323, M.324, F.327, L.328 Ligands: P9P.4, P9P.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.180, A:L.320, A:F.327 Hydrogen bonds: A:Y.163, A:Y.163, A:N.277 P9P.4: 8 residues within 4Å: Chain A: W.126, L.180, D.183, Y.362 Ligands: P9P.3, P9P.5, P9P.6, P9P.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.126 Hydrogen bonds: A:Y.362 pi-Stacking: A:Y.362 P9P.5: 9 residues within 4Å: Chain A: L.180, V.186, A.187, F.273, L.276, L.320 Ligands: SAH.2, P9P.3, P9P.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.180, A:L.180, A:F.273 pi-Stacking: A:F.273 P9P.6: 10 residues within 4Å: Chain A: A.121, Q.123, D.183, T.359, I.360 Chain B: L.37, I.41 Ligands: P9P.4, P9P.7, SO4.9 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.121, A:D.183, A:I.360, B:L.37 Hydrogen bonds: A:D.183, A:T.359 P9P.7: 10 residues within 4Å: Chain A: E.315, Q.316, E.319, I.360, Y.362 Chain B: R.38, I.41 Ligands: P9P.4, P9P.6, SO4.9 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.41, A:Q.316 P9P.13: 13 residues within 4Å: Chain B: W.126, V.133, F.162, Y.163, F.176, N.277, L.320, R.323, M.324, F.327, L.328 Ligands: P9P.14, P9P.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.176, B:L.320 Hydrogen bonds: B:Y.163, B:N.277 P9P.14: 8 residues within 4Å: Chain B: L.180, F.188, F.273, L.276, L.320 Ligands: SAH.12, P9P.13, P9P.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.180, B:F.273 pi-Stacking: B:F.273 P9P.15: 6 residues within 4Å: Chain B: W.126, D.183, I.360, Y.362 Ligands: P9P.13, P9P.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.126 Hydrogen bonds: B:Y.362 Water bridges: B:D.183 pi-Stacking: B:Y.362

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

SAH.2: 17 residues within 4Å: Chain A: Y.163, R.173, L.180, 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 Ligands: P9P.5 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:G.207, A:D.257, A:D.257, A:F.258 Water bridges: A:D.177, A:S.272, A:S.272, A:S.272 pi-Stacking: A:Y.163, A:F.258 SAH.12: 18 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 Ligands: P9P.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.173, B:R.173, B:G.207, B:D.257, B:D.257, B:F.258 Water bridges: B:D.177, B:S.272 pi-Stacking: B:Y.163, B:F.258

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

SO4.8: 4 residues within 4Å: Chain A: R.151, P.279, H.281 Chain B: R.81 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:D.280 Salt bridges: A:R.151, B:R.81 SO4.9: 7 residues within 4Å: Chain A: Q.123, W.126, E.319, R.323 Chain B: I.41 Ligands: P9P.6, P9P.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.123 Water bridges: A:R.323, A:R.323, A:R.323 Salt bridges: A:R.323 SO4.10: 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 SO4.11: 3 residues within 4Å: Chain A: R.81, P.82, E.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.83 Salt bridges: A:R.81 SO4.16: 2 residues within 4Å: Chain B: R.135, R.169 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.169, B:R.169 Salt bridges: B:R.135, B:R.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, T.D. et al., Functional AdoMet Isosteres Resistant to Classical AdoMet Degradation Pathways. Acs Chem.Biol. (2016)

Release Date

2015-12-16

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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