SMTL ID : 6ojr.1

Crystal structure of Sphingomonas paucimobilis TMY1009 apo-LsdA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: A.126, K.128, Y.130, I.140, T.152, F.154, T.199, G.200, K.201 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.130, A:T.152, A:T.152, A:T.199 GOL.2: 5 residues within 4Å: Chain A: Q.209, N.210, P.211, Y.256, W.271 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.210, A:P.211 GOL.3: 3 residues within 4Å: Chain A: A.1, H.2, P.49 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Water bridges: B:D.24, A:A.1, A:A.1, A:A.1, A:H.2, A:P.50 Hydrogen bonds: A:H.2, A:H.2 GOL.7: 4 residues within 4Å: Chain B: Q.209, P.211, Y.256, W.271 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.209 Water bridges: B:Q.209 GOL.8: 11 residues within 4Å: Chain B: F.58, Y.100, R.101, T.120, K.133, E.134, D.135, Y.181, M.215, H.217, F.247 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.58, B:R.101, B:R.101 Water bridges: B:E.134

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: R.346, D.371, K.374, T.389, W.404 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.371, A:T.389 MG.5: 3 residues within 4Å: Chain A: R.352, I.353, E.355 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.355, H2O.6 MG.6: 5 residues within 4Å: Chain A: T.387, A.410, I.411, Q.412, Q.468 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:I.411

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuatsjah, E. et al., Identification of functionally important residues and structural features in a bacterial lignostilbene dioxygenase. J.Biol.Chem. (2019)

Release Date

2019-07-24

Peptides

Lignostilbene-alpha,beta-dioxygenase isozyme I: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lignostilbene-alpha,beta-dioxygenase isozyme I