SMTL ID : 6p3j.1

Crystal structure of LigU

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: I.276, P.277, H.278, R.279 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: C.100, G.101, V.286, L.287 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: D.220, R.221 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: P.62, F.88, V.89 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: R.28, A.29, V.70, S.71 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: R.28, A.29, V.70, S.71 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: P.62, F.88, V.89 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain B: N.99, C.100, G.101, V.286, L.287 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain B: I.276, P.277, H.278, R.279 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 2 residues within 4Å: Chain B: R.6, E.359 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:R.6, B:E.359, B:E.359, H2O.6, H2O.7 CA.7: 3 residues within 4Å: Chain B: M.8, D.9, E.359 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:M.8, B:D.9, B:E.359, H2O.7, H2O.8

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

NA.12: 1 residues within 4Å: Chain B: R.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.3, A:E.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hogancamp, T.N. et al., Structure and Chemical Reaction Mechanism of LigU, an Enzyme That Catalyzes an Allylic Isomerization in the Bacterial Degradation of Lignin. Biochemistry (2019)

Release Date

2019-07-31

Peptides

(4E)-oxalomesaconate Delta-isomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

(4E)-oxalomesaconate Delta-isomerase