SMTL ID : 3wrb.1

Crystal structure of the anaerobic H124F DESb-Gallate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.12, N.57, H.59, E.239 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.12, A:H.59, A:E.239, H2O.2, H2O.2 FE2.3: 4 residues within 4Å: Chain B: H.12, N.57, H.59, E.239 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.12, B:H.59, B:E.239, H2O.11, H2O.13

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

GDE.2: 12 residues within 4Å: Chain A: F.374, E.377, N.387, Y.391 Chain B: T.13, P.14, T.15, F.124, H.192, V.194, M.266, T.267 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:P.14, B:V.194 Hydrogen bonds: B:T.267, A:E.377, A:N.387, A:Y.391 Water bridges: B:T.267, B:T.267 GDE.4: 13 residues within 4Å: Chain A: T.13, P.14, T.15, F.124, H.192, V.194, M.266, T.267 Chain B: F.373, F.374, E.377, N.387, Y.391 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:E.377, B:N.387, A:T.13, A:T.267, A:T.267 Hydrophobic interactions: A:P.14, A:V.194 Water bridges: A:H.192, A:H.192, A:H.192

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