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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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, 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.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.173, A:R.173, A:G.207, A:D.257, A:D.257, A:F.258, A:S.272 Water bridges: A:S.272, A:S.272, A:S.272, A:S.272 pi-Stacking: A:Y.163, A:F.258 SAH.12: 17 residues within 4Å: Chain B: 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.15 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:R.173, B:R.173, B:G.207, B:D.257, B:F.258, B:S.272 Water bridges: B:S.272, B:S.272, B:S.272, B:H.303 pi-Stacking: B:Y.163, B:F.258

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

P9P.2: 13 residues within 4Å: Chain A: W.126, V.133, F.162, Y.163, F.176, N.277, L.320, R.323, M.324, F.327, L.328 Ligands: P9P.3, P9P.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.176, A:L.320, A:F.327 Hydrogen bonds: A:Y.163, A:N.277 P9P.3: 10 residues within 4Å: Chain A: W.126, L.180, D.183, V.186, Y.362 Ligands: P9P.2, P9P.4, P9P.5, P9P.6, SO4.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.126 Hydrogen bonds: A:Y.362 pi-Stacking: A:Y.362 P9P.4: 9 residues within 4Å: Chain A: L.180, V.186, A.187, F.273, L.276, L.320 Ligands: SAH.1, P9P.2, P9P.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.180, A:F.273 pi-Stacking: A:F.273 P9P.5: 10 residues within 4Å: Chain A: A.121, Q.123, D.183, T.359, I.360 Chain B: L.37, I.41 Ligands: P9P.3, P9P.6, SO4.9 5 PLIP interactions: 4 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:T.359 P9P.6: 9 residues within 4Å: Chain A: Q.316, E.319, I.360, Y.362 Chain B: R.38, I.41 Ligands: P9P.3, P9P.5, SO4.9 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.316, B:I.41, B:I.41 Water bridges: A:Y.362 P9P.7: 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.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 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.176, B:L.320, B:F.327 Hydrogen bonds: B:Y.163, B:Y.163, B:N.277 P9P.14: 10 residues within 4Å: Chain B: W.126, L.180, D.183, V.186, Y.362 Ligands: P9P.13, P9P.15, P9P.16, P9P.17, SO4.20 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.126 Hydrogen bonds: B:Y.362 pi-Stacking: B:Y.362 P9P.15: 9 residues within 4Å: Chain B: L.180, V.186, A.187, F.273, L.276, L.320 Ligands: SAH.12, P9P.13, P9P.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.180, B:F.273 pi-Stacking: B:F.273 P9P.16: 10 residues within 4Å: Chain A: L.37, I.41 Chain B: A.121, Q.123, D.183, T.359, I.360 Ligands: P9P.14, P9P.17, SO4.20 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.121, B:D.183, B:I.360, A:L.37 Hydrogen bonds: B:D.183 P9P.17: 9 residues within 4Å: Chain A: R.38, I.41 Chain B: Q.316, E.319, I.360, Y.362 Ligands: P9P.14, P9P.16, SO4.20 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.41, A:I.41, B:Q.316 P9P.18: 2 residues within 4Å: Chain B: A.193, R.220 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:R.220 Hydrogen bonds: B:R.220 Water bridges: B:D.189

8 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 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.281 Water bridges: A:D.280 Salt bridges: A:R.151, B:R.81 SO4.9: 8 residues within 4Å: Chain A: Q.123, W.126, E.319, R.323 Chain B: I.41 Ligands: P9P.3, P9P.5, P9P.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.123, A:Q.123 Water bridges: A:R.323, A:R.323 Salt bridges: A:R.323 SO4.10: 2 residues within 4Å: Chain A: R.135, R.169 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.135, A:R.135, A:R.169, A:R.169 Salt bridges: A:R.135, A:R.169 SO4.11: 3 residues within 4Å: Chain A: H.63, A.66, R.77 4 PLIP interactions: 4 interactions with chain A Water bridges: A:H.63, A:R.77 Salt bridges: A:H.63, A:R.77 SO4.19: 4 residues within 4Å: Chain A: R.81 Chain B: R.151, P.279, H.281 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.281 Water bridges: B:D.280 Salt bridges: B:R.151, A:R.81 SO4.20: 8 residues within 4Å: Chain A: I.41 Chain B: Q.123, W.126, E.319, R.323 Ligands: P9P.14, P9P.16, P9P.17 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.123, B:Q.123 Water bridges: B:E.319, B:R.323 Salt bridges: B:R.323 SO4.21: 2 residues within 4Å: Chain B: R.135, R.169 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.135, B:R.135, B:R.169, B:R.169 Salt bridges: B:R.135, B:R.169 SO4.22: 3 residues within 4Å: Chain B: H.63, A.66, R.77 4 PLIP interactions: 4 interactions with chain B Water bridges: B:H.63, B:R.77 Salt bridges: B:H.63, B:R.77

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
A

B
A

Carminomycin 4-O-methyltransferase DnrK

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