SMTL ID : 4zlu.1

Lipomyces starkeyi levoglucosan kinase bound to levoglucosan, ADP and magnesium.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 20 residues within 4Å: Chain A: G.22, T.23, S.24, M.25, D.26, G.188, G.189, N.217, D.221, Y.234, D.235, K.236, D.237, G.327, G.328, G.329, Y.331, E.362 Ligands: MG.3, MG.4 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:G.22, A:T.23, A:S.24, A:S.24, A:M.25, A:G.189, A:D.221, A:D.237, A:D.237, A:D.237, A:G.328 Water bridges: A:N.20, A:T.23, A:T.23, A:D.26, A:G.27, A:D.29, A:N.186, A:I.190, A:D.221, A:E.362, A:E.362 ADP.5: 13 residues within 4Å: Chain B: G.22, T.23, S.24, D.26, G.188, G.189, N.217, D.221, Y.234, G.327, G.328, Y.331, E.362 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:G.22, B:G.22, B:T.23, B:T.23, B:S.24, B:S.24, B:D.29, B:G.189, B:D.221, B:Y.234, B:G.328 Water bridges: B:G.27, B:N.186, B:G.188, B:I.190, B:D.221, B:D.221, B:D.221, B:D.237, B:E.362, B:E.362 pi-Stacking: B:Y.234, B:Y.234

2 x 4PW: Levoglucosan(Non-covalent)

4PW.2: 8 residues within 4Å: Chain A: R.153, A.164, P.165, N.186, I.190, N.192, D.212, E.362 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.153, A:R.153, A:E.362 Water bridges: A:R.153, A:P.165, A:G.189, A:I.190, A:N.192, A:T.268, A:E.362 4PW.7: 9 residues within 4Å: Chain B: R.153, A.164, P.165, N.186, I.190, N.192, D.212, T.268, E.362 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.186, B:N.192, B:D.212, B:D.212 Water bridges: B:R.153, B:R.153, B:G.188, B:N.192, B:N.192 Salt bridges: B:R.153

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: N.186, E.362 Ligands: ADP.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.362, A:E.362, H2O.2, H2O.12, H2O.13 MG.4: 4 residues within 4Å: Chain A: G.22, D.26, D.29 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.26, H2O.2, H2O.2, H2O.7

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 7 residues within 4Å: Chain B: L.173, L.174, H.176, E.424, T.435, N.436, N.437 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:L.173, B:N.436, B:N.437, B:N.437 Water bridges: B:E.424, B:I.434, B:N.436

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bacik, J.P. et al., Producing Glucose 6-Phosphate from Cellulosic Biomass: STRUCTURAL INSIGHTS INTO LEVOGLUCOSAN BIOCONVERSION. J.Biol.Chem. (2015)

Release Date

2015-09-16

Peptides

Levoglucosan kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Levoglucosan kinase

Related Entries With Identical Sequence