SMTL ID : 4xt0.1

Crystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x GSH: GLUTATHIONE(Non-covalent)

GSH.1: 12 residues within 4Å: Chain A: F.11, A.15, N.16, Q.43, H.44, Q.56, V.57, P.58, E.69, S.70, Q.148, W.152 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.16, A:Q.43, A:Q.56, A:V.57, A:V.57, A:E.69, A:E.69, A:S.70, A:Q.148 Water bridges: A:T.71, B:K.104, B:K.104 Salt bridges: A:H.44, B:K.104 GSH.4: 12 residues within 4Å: Chain B: F.11, A.15, N.16, Q.43, H.44, Q.56, V.57, P.58, E.69, S.70, Q.148, W.152 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.16, B:Q.43, B:Q.56, B:V.57, B:V.57, B:E.69, B:E.69, B:S.70, B:Q.148 Water bridges: B:T.71, B:D.107, A:K.104 Salt bridges: B:H.44, A:K.104

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 8 residues within 4Å: Chain A: L.24, Y.25, G.28, L.29, E.30, F.31, E.241, K.245 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.24, A:G.28, A:E.241, A:K.245 Water bridges: A:Y.25 TRS.5: 8 residues within 4Å: Chain B: L.24, Y.25, G.28, L.29, E.30, F.31, E.241, K.245 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.24, B:G.28, B:E.241, B:E.241, B:K.245

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 6 residues within 4Å: Chain A: E.98, V.101, W.102, W.105, R.177 Chain B: R.54 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.177 Water bridges: A:T.181, A:T.181 1PE.6: 6 residues within 4Å: Chain A: R.54 Chain B: E.98, V.101, W.102, W.105, R.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.177 Water bridges: B:R.177, B:T.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Helmich, K.E. et al., Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin. J.Biol.Chem. (2016)

Release Date

2016-02-03

Peptides

Protein LigF: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Protein LigF