SMTL ID : 8bid.2 (1 other biounit)

O-Methyltransferase Plu4890 (mutant H229N) in complex with SAH and AQ-270a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 16 residues within 4Å: Chain A: F.127, F.140, M.144, S.148, G.171, G.172, G.173, D.194, R.195, G.210, N.211, F.212, K.226, N.227, N.231, W.232 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.171, A:N.211, A:F.212, A:K.226, A:N.227 Water bridges: A:K.137, A:S.148, A:K.226 Salt bridges: A:K.226 pi-Stacking: A:F.212 pi-Cation interactions: A:R.195 SAH.12: 16 residues within 4Å: Chain B: F.127, M.144, S.148, G.171, G.173, L.193, D.194, R.195, G.210, N.211, F.212, L.213, K.226, N.227, N.231, W.232 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.171, B:R.195, B:N.211, B:F.212, B:K.226, B:N.227 Water bridges: B:K.226 Salt bridges: B:K.226 pi-Stacking: B:F.127, B:F.212

2 x QPF: 1-methoxy-3,8-bis(oxidanyl)anthracene-9,10-dione(Non-covalent)

QPF.2: 13 residues within 4Å: Chain A: M.89, F.140, L.143, M.144, N.227, N.230, N.231, F.269, M.273, L.276, F.277 Ligands: NA.10, GOL.25 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.140 Hydrogen bonds: A:N.227, A:N.230, A:N.231, B:R.11 Water bridges: A:M.89, A:E.93 pi-Stacking: A:F.269, A:F.269 QPF.13: 15 residues within 4Å: Chain B: M.89, Y.98, F.140, L.143, M.144, N.227, N.230, N.231, M.259, F.269, L.272, M.273, L.276 Ligands: GOL.11, NA.21 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.143 Hydrogen bonds: B:N.227, B:N.230, B:N.231, A:R.11 Water bridges: B:E.93, B:E.93, B:Y.98, B:N.227 pi-Stacking: B:F.269, B:F.269

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 4 residues within 4Å: Chain A: H.189, A.191, D.206, Y.220 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: R.166, H.189, A.191, D.206, Y.220 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: R.71, S.73, D.74 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: E.176, R.180 Ligand excluded by PLIP

15 x NA: SODIUM ION(Non-functional Binders)

NA.4: 3 residues within 4Å: Chain A: F.88, K.91, N.139 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.91, A:K.91, A:N.139 NA.5: 2 residues within 4Å: Chain A: S.235, D.236 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.236 NA.6: 5 residues within 4Å: Chain A: D.169, G.172, G.175, L.177, L.178 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.175, A:L.177, A:L.178 Water bridges: A:E.176 NA.7: 2 residues within 4Å: Chain A: E.86 Chain B: L.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.86, A:E.86 NA.8: 5 residues within 4Å: Chain A: F.28, G.31, I.32, R.71, L.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.32, A:L.72 Water bridges: A:G.31 NA.9: 6 residues within 4Å: Chain A: S.99, N.100, L.103 Chain B: S.96, S.99 Ligands: NA.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100 NA.10: 5 residues within 4Å: Chain A: V.147, M.259, Y.308, Y.311 Ligands: QPF.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.227, A:Y.311 NA.17: 6 residues within 4Å: Chain A: S.96, S.99 Chain B: S.99, N.100, L.103 Ligands: NA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100 NA.18: 2 residues within 4Å: Chain B: D.67, N.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.67, B:N.68 NA.19: 5 residues within 4Å: Chain B: F.28, G.31, I.32, R.71, L.72 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.31, B:L.72 Water bridges: B:G.31 NA.20: 2 residues within 4Å: Chain B: S.37, R.41 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.40, B:R.41 NA.21: 5 residues within 4Å: Chain B: V.147, M.259, Y.308, Y.311 Ligands: QPF.13 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.308, B:Y.308, B:Y.311 NA.22: 3 residues within 4Å: Chain B: H.17, K.91, F.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.91 NA.23: 3 residues within 4Å: Chain B: F.88, K.91, N.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.91, B:N.139, B:N.139 NA.24: 4 residues within 4Å: Chain B: P.82, S.87, F.88, K.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.82

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 9 residues within 4Å: Chain A: T.4, E.5, R.11 Chain B: M.89, M.259, S.268, F.269, Y.308 Ligands: QPF.13 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.4, A:R.11, A:R.11, B:S.268 Water bridges: B:F.269 GOL.25: 9 residues within 4Å: Chain A: M.89, M.259, S.268, F.269, Y.308 Chain B: T.4, E.5, R.11 Ligands: QPF.2 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.4, B:R.11, B:R.11, A:S.268 Water bridges: A:F.269 GOL.26: 5 residues within 4Å: Chain B: D.21, T.22, G.23, P.82, K.91 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.21, B:D.21, B:K.91 Water bridges: B:G.23 GOL.27: 8 residues within 4Å: Chain A: M.2, L.3, L.6 Chain B: M.60, G.61, S.73, E.75, C.76 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:M.2, B:G.61, B:S.73, B:S.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, E.M. et al., A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Structure (2023)

Release Date

2023-03-08

Peptides

methyltransferase Plu4890 H229N mutant: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

methyltransferase Plu4890 H229N mutant

Related Entries With Identical Sequence