SMTL ID : 6c5b.1

Crystal Structure Analysis of LaPhzM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

homo-dimer

Ligands

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

SAH.1: 20 residues within 4Å: Chain A: F.138, Q.155, T.159, G.182, A.183, G.184, F.204, D.205, Q.206, V.209, G.231, D.232, F.233, F.234, S.247, L.248, L.249, D.252, W.253 Ligands: FMT.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Q.155 Hydrogen bonds: A:Q.155, A:T.159, A:G.184, A:Q.206, A:Q.206, A:D.232, A:F.233, A:S.247, A:S.247 Water bridges: A:N.152, A:N.152, A:S.247 pi-Stacking: A:F.138, A:F.233 SAH.8: 19 residues within 4Å: Chain B: F.138, Q.155, T.159, G.182, A.183, G.184, D.205, Q.206, V.209, G.231, D.232, F.233, F.234, S.247, L.248, L.249, D.252, W.253 Ligands: FMT.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.155 Hydrogen bonds: B:N.152, B:G.182, B:G.184, B:Q.206, B:Q.206, B:D.232, B:F.233, B:S.247 Water bridges: B:D.252 pi-Stacking: B:F.138, B:F.233

3 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 8 residues within 4Å: Chain A: D.180, A.183, G.186, P.187, L.188, L.189, S.247 Ligands: SAH.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.188, A:L.189 Water bridges: A:D.180, A:S.247 FMT.3: 4 residues within 4Å: Chain A: H.144, P.145, E.146, A.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.146, A:A.147 FMT.9: 8 residues within 4Å: Chain B: D.180, A.183, G.186, P.187, L.188, L.189, S.247 Ligands: SAH.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.186, B:L.188, B:L.189 Water bridges: B:S.247

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

NA.4: 5 residues within 4Å: Chain A: K.292, D.295, L.296 Chain B: R.64, T.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.295, A:D.295 NA.5: 2 residues within 4Å: Chain A: G.108 Chain B: A.116 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.116 NA.6: 5 residues within 4Å: Chain A: R.64, T.68 Chain B: K.292, D.295, L.296 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.64

1 x P33: 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL(Non-covalent)

P33.7: 13 residues within 4Å: Chain A: Q.18, M.19, T.21, V.25, I.72, F.290, W.293 Chain B: Q.18, M.19, T.21, V.25, I.72, W.293 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.18, A:T.21, B:Q.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jiang, J. et al., Functional and Structural Analysis of Phenazine O-Methyltransferase LaPhzM from Lysobacter antibioticus OH13 and One-Pot Enzymatic Synthesis of the Antibiotic Myxin. ACS Chem. Biol. (2018)

Release Date

2018-03-21

Peptides

Methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Methyltransferase