SMTL ID : 4yh5.1

Lipomyces starkeyi levoglucosan kinase bound to ADP and Manganese

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 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: MN.2, MN.3 21 PLIP interactions: 21 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:D.26, A:D.29, A:G.188, A:I.190, A:D.221, A:N.332, A:E.362, A:E.362 ADP.4: 20 residues within 4Å: Chain B: 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: MN.5, MN.6 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:G.22, B:S.24, B:S.24, B:M.25, B:G.189, B:D.221, B:D.237, B:D.237, B:G.328 Water bridges: B:N.20, B:N.20, B:T.23, B:D.26, B:G.27, B:N.186, B:G.188, B:I.190, B:Y.234

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 2 residues within 4Å: Chain A: 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.1, H2O.14, H2O.15 MN.3: 3 residues within 4Å: Chain A: 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.1, H2O.2, H2O.5 MN.5: 2 residues within 4Å: Chain B: E.362 Ligands: ADP.4 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.362, B:E.362, H2O.23, H2O.34, H2O.35 MN.6: 3 residues within 4Å: Chain B: D.26, D.29 Ligands: ADP.4 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.26, H2O.22, H2O.23, H2O.24

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

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

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

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