SMTL ID : 3wku.1

Crystal structure of the anaerobic DesB-gallate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x FE: FE (III) ION(Non-covalent)

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

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

GDE.2: 14 residues within 4Å: Chain A: F.374, E.377, Y.391, Y.412 Chain B: T.13, P.14, T.15, H.59, H.124, H.192, V.194, E.239, T.267 Ligands: FE.3 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:T.13, B:P.14, B:V.194 Hydrogen bonds: B:H.124, A:E.377, A:Y.391, A:Y.391 Water bridges: B:N.57

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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