SMTL ID : 3wr9.1

Crystal structure of the Anaerobic DesB-Gallate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.12, H.59, E.239 Ligands: GDE.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.12, A:H.59, H2O.4 FE2.2: 2 residues within 4Å: Chain A: H.20, H.136 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.20, A:H.136 FE2.4: 5 residues within 4Å: Chain B: H.12, N.57, H.59, E.239 Ligands: GDE.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.12, B:H.59, B:E.239, H2O.5 FE2.5: 3 residues within 4Å: Chain B: H.20, L.90, H.136 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.20, B:H.136, H2O.4

2 x GDE: 3,4,5-trihydroxybenzoic acid(Non-covalent)

GDE.3: 16 residues within 4Å: Chain A: H.12, T.13, P.14, H.59, H.124, H.192, V.194, E.239, M.266, T.267 Chain B: F.374, E.377, N.387, Y.391, Y.412 Ligands: FE2.1 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:P.14, A:V.194 Water bridges: A:T.13, A:E.239, A:M.266 Hydrogen bonds: B:E.377, B:N.387, B:Y.391, B:Y.391, B:Y.412 GDE.6: 17 residues within 4Å: Chain A: F.374, E.377, N.387, Y.391, Y.412 Chain B: H.12, T.13, P.14, T.15, H.59, H.124, H.192, V.194, E.239, M.266, T.267 Ligands: FE2.4 11 PLIP interactions: 2 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:E.377, A:N.387, B:T.13, B:H.124, B:T.267, B:T.267 Hydrophobic interactions: B:P.14, B:V.194 Water bridges: B:T.13, B:E.239, B:T.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugimoto, K. et al., Molecular Mechanism of Strict Substrate Specificity of an Extradiol Dioxygenase, DesB, Derived from Sphingobium sp. SYK-6. Plos One (2014)

Release Date

2014-04-30

Peptides

Gallate dioxygenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Gallate dioxygenase

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