SMTL ID : 5t64.1

X-ray structure of the C3-methyltransferase KijD1 from Actinomadura kijaniata in complex with TDP and SAH

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.15, C.18, C.56, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.18, A:C.56, A:C.59 ZN.7: 4 residues within 4Å: Chain B: C.15, C.18, C.56, C.59 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.15, B:C.18, B:C.56, B:C.59

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

SAH.2: 19 residues within 4Å: Chain A: F.74, Y.78, S.82, F.92, I.114, G.115, N.117, F.135, E.136, P.137, S.138, F.156, F.157, A.178, N.179, T.180, H.183, I.184, Y.186 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:N.117 Hydrogen bonds: A:S.82, A:G.115, A:G.115, A:N.117, A:S.138, A:S.138, A:F.157, A:F.157, A:N.179 Water bridges: A:A.178, A:Y.186 pi-Stacking: A:F.74 SAH.8: 17 residues within 4Å: Chain B: S.82, F.92, I.114, G.115, N.117, F.135, E.136, P.137, S.138, F.156, F.157, A.178, N.179, T.180, H.183, I.184, Y.186 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:N.117 Hydrogen bonds: B:S.82, B:G.115, B:G.115, B:N.117, B:S.138, B:F.157, B:F.157, B:N.179, B:T.180, B:Y.186 Water bridges: B:R.70, B:A.178

3 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: D.27, R.50 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.27, H2O.7, H2O.10

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.6: 13 residues within 4Å: Chain A: Y.325, G.326, A.327, T.328, A.329, D.350, T.351, T.352, K.355, A.385, H.388, I.392, K.395 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:H.388 Hydrogen bonds: A:A.329, A:T.351, A:T.352, A:K.355, A:K.395 Water bridges: A:Y.325, A:Y.325, A:K.330, A:K.355, A:N.387 Salt bridges: A:K.330, A:K.355 TMP.11: 14 residues within 4Å: Chain B: Y.325, G.326, A.327, T.328, A.329, D.350, T.351, T.352, K.355, A.385, H.388, E.391, I.392, K.395 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.388, B:I.392 Hydrogen bonds: B:A.329, B:T.351, B:T.352, B:K.355, B:K.395 Water bridges: B:H.256, B:Y.325, B:K.330, B:K.330, B:T.351, B:K.395 Salt bridges: B:K.330

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 4 residues within 4Å: Chain B: V.248, R.270, T.271, T.273 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.270, B:T.271 Water bridges: B:T.271 EDO.10: 7 residues within 4Å: Chain B: H.91, K.94, V.95, R.98, E.251, L.253, R.261 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:H.91, B:E.251, B:R.261, B:R.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dow, G.T. et al., Structural studies on KijD1, a sugar C-3'-methyltransferase. Protein Sci. (2016)

Release Date

2016-09-14

Peptides

Sugar 3-C-methyl transferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sugar 3-C-methyl transferase

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