SMTL ID : 5ufm.3 (2 other biounits)

Crystal structure of Burkholderia thailandensis 1,6-didemethyltoxoflavin-N1-methyltransferase with bound 1,6-didemethyltoxoflavin and S-adenosylhomocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: L.34, F.38, Y.42, W.49, M.55, G.76, A.77, G.78, R.81, D.82, D.97, L.98, C.120, P.121, V.122, N.137, G.138, C.139, Q.143 Ligands: AZ8.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:Y.42, A:G.78, A:L.98, A:V.122, A:N.137, A:N.137, A:Q.143, A:Q.143 Water bridges: A:Y.42, A:R.79, A:R.81, A:D.82, A:S.123, A:N.137 Salt bridges: A:R.81 SAH.12: 21 residues within 4Å: Chain B: L.34, F.38, Y.42, W.49, M.55, G.76, A.77, G.78, R.81, D.82, D.97, L.98, V.99, C.120, P.121, V.122, N.137, G.138, C.139, Q.143 Ligands: AZ8.13 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:Y.42, B:G.78, B:L.98, B:V.122, B:N.137, B:N.137, B:Q.143, B:Q.143 Water bridges: B:Y.42, B:R.79, B:R.81, B:D.82, B:N.137 Salt bridges: B:R.81

2 x AZ8: pyrimido[5,4-e][1,2,4]triazine-5,7(6H,8H)-dione(Non-covalent)

AZ8.2: 12 residues within 4Å: Chain A: D.12, R.15, W.49, G.138, H.141, H.142, F.170, R.185, Y.187, R.214, Y.221 Ligands: SAH.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.12, A:D.12, A:H.142, A:R.185, A:R.185, A:R.214 Water bridges: A:Y.221 pi-Stacking: A:F.170 AZ8.13: 12 residues within 4Å: Chain B: D.12, W.49, M.55, G.138, H.141, H.142, F.170, R.185, Y.187, R.214, Y.221 Ligands: SAH.12 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.12, B:D.12, B:H.142, B:R.185, B:R.214, B:Y.221 pi-Stacking: B:F.170, B:F.170

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

SO4.3: 3 residues within 4Å: Chain A: H.65, R.164, V.207 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.65, A:R.164 Water bridges: B:A.64, B:A.64 SO4.4: 4 residues within 4Å: Chain A: E.128, H.156, A.157, K.228 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.156 Water bridges: A:A.157, A:K.228, A:K.228 Salt bridges: A:H.156, A:K.228 SO4.5: 4 residues within 4Å: Chain A: T.205, R.227, T.229, D.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.230 Salt bridges: A:R.227 SO4.6: 2 residues within 4Å: Chain A: R.92, R.114 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.92, A:R.114 SO4.7: 2 residues within 4Å: Chain A: R.110, W.111 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.110 SO4.10: 6 residues within 4Å: Chain A: E.52, A.53, A.54, P.215, K.216 Chain B: R.56 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:A.53, A:A.54, A:K.216 Water bridges: A:E.52, A:E.52, B:R.56, B:R.56 Salt bridges: A:K.216, B:R.56 SO4.11: 6 residues within 4Å: Chain A: R.56 Chain B: E.52, A.53, A.54, P.215, K.216 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.53, B:A.54, B:K.216 Water bridges: B:D.51, B:K.216, B:A.217, A:R.56 Salt bridges: A:R.56 SO4.14: 3 residues within 4Å: Chain B: H.65, R.164, V.207 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.65, B:R.164 SO4.15: 3 residues within 4Å: Chain B: H.156, A.157, K.228 5 PLIP interactions: 5 interactions with chain B Water bridges: B:H.156, B:K.228, B:K.228 Salt bridges: B:H.156, B:K.228 SO4.16: 4 residues within 4Å: Chain B: T.205, R.227, T.229, D.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.205, B:D.230 Salt bridges: B:R.227 SO4.17: 2 residues within 4Å: Chain B: R.92, R.114 5 PLIP interactions: 5 interactions with chain B Water bridges: B:G.90, B:R.114, B:R.114 Salt bridges: B:R.92, B:R.114

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

EPE.8: 5 residues within 4Å: Chain A: S.40, D.44, R.46, H.182, A.183 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.46 Water bridges: A:S.40, A:R.46, A:H.182, A:A.183 Salt bridges: A:D.44, A:D.44, A:H.182 EPE.9: 2 residues within 4Å: Chain A: E.100, P.102 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.100 Salt bridges: A:E.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fenwick, M.K. et al., Biochemical Characterization and Structural Basis of Reactivity and Regioselectivity Differences between Burkholderia thailandensis and Burkholderia glumae 1,6-Didesmethyltoxoflavin N-Methyltransferase. Biochemistry (2017)

Release Date

2017-12-13

Peptides

Methyltransferase domain protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase domain protein

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