SMTL ID : 5tkr.1

Crystal structure of a Lipomyces starkeyi levoglucosan kinase G359R mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 23 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, R.359, E.362 Ligands: MG.2, MG.3, SO4.4, K.6 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.22, A:S.24, A:S.24, A:M.25, A:G.189, A:D.221, A:D.237, A:D.237, A:G.328, A:R.359, A:R.359 Water bridges: A:N.20, A:D.26, A:D.29, A:D.29, A:D.29, A:N.332, A:E.362 ADP.7: 23 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, R.359, E.362 Ligands: MG.8, MG.9, SO4.10, K.12 20 PLIP interactions: 20 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:D.237, B:G.328, B:R.359, B:R.359 Water bridges: B:N.20, B:D.26, B:D.29, B:D.29, B:D.29, B:D.221, B:N.332, B:E.362

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.26 Ligands: ADP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.26, H2O.2, H2O.3, H2O.6 MG.3: 3 residues within 4Å: Chain A: E.362 Ligands: ADP.1, SO4.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.362, A:E.362, H2O.1, H2O.5 MG.8: 2 residues within 4Å: Chain B: D.26 Ligands: ADP.7 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.26, H2O.20, H2O.20, H2O.23 MG.9: 3 residues within 4Å: Chain B: E.362 Ligands: ADP.7, SO4.10 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.362, B:E.362, H2O.19, H2O.23

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 9 residues within 4Å: Chain A: G.22, T.23, N.186, G.188, G.189, I.190, E.362 Ligands: ADP.1, MG.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.23, A:N.186, A:G.189, A:I.190, A:I.190 SO4.10: 9 residues within 4Å: Chain B: G.22, T.23, N.186, G.188, G.189, I.190, E.362 Ligands: ADP.7, MG.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.23, B:N.186, B:G.189, B:I.190, B:I.190

4 x K: POTASSIUM ION(Non-covalent)

K.5: 5 residues within 4Å: Chain A: L.174, L.175, H.176, N.436, N.437 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.176, H2O.9, H2O.14 K.6: 5 residues within 4Å: Chain A: D.29, Y.51, E.53, R.359 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.29, A:E.53, H2O.4, H2O.4 K.11: 5 residues within 4Å: Chain B: L.174, L.175, H.176, N.436, N.437 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.176, H2O.27, H2O.31 K.12: 5 residues within 4Å: Chain B: D.29, Y.51, E.53, R.359 Ligands: ADP.7 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.29, B:E.53, H2O.22, H2O.22

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klesmith, J.R. et al., Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-02-08

Peptides

Levoglucosan kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Levoglucosan kinase