SMTL ID : 9f3n.1

Crystal structure of the intermediate open state of apo Kluyveromyces lactis glucokinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

10 x MLI: MALONATE ION(Non-functional Binders)

MLI.1: 7 residues within 4Å: Chain A: G.78, G.79, T.80, N.81, R.83, K.170 Ligands: MLI.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.78, A:G.79, A:T.80, A:N.81, A:N.81, A:R.83 Salt bridges: A:R.83, A:K.170 MLI.2: 4 residues within 4Å: Chain A: Y.30, K.50, N.282, H.283 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.30 Salt bridges: A:K.37, A:K.50, A:H.283 MLI.3: 8 residues within 4Å: Chain A: K.170, I.233, G.235, T.236, G.237, G.429, S.430 Ligands: MLI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.235, A:T.236, A:G.237, A:S.430 Salt bridges: A:K.170 MLI.4: 3 residues within 4Å: Chain A: K.245, N.248, K.411 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.248 Salt bridges: A:K.245, A:K.411 MLI.5: 8 residues within 4Å: Chain A: R.395, F.399, S.440, M.441, H.444 Chain B: H.420, Q.422, D.458 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.395, A:S.440, B:H.420, B:D.458 Salt bridges: A:R.395, A:H.444, B:H.420 MLI.6: 8 residues within 4Å: Chain A: H.420, Q.422, D.458 Chain B: R.395, F.399, S.440, M.441, H.444 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.440, B:S.440 Salt bridges: B:R.395, B:R.395, B:H.444, A:H.420 MLI.7: 8 residues within 4Å: Chain B: G.78, G.79, T.80, N.81, R.83, K.170, T.236 Ligands: MLI.10 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.79, B:T.80, B:T.80, B:N.81 Salt bridges: B:R.83, B:K.170 MLI.8: 9 residues within 4Å: Chain B: T.169, K.170, G.171, S.298, T.299, N.300, K.308, L.313, Y.314 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.169, B:S.298, B:T.299, B:T.299, B:N.300, B:N.300, B:Y.314, B:Y.314 Salt bridges: B:K.308 MLI.9: 8 residues within 4Å: Chain B: G.312, T.348, E.349, S.352, S.430, V.431, H.434, Y.435 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.348 Hydrogen bonds: B:S.430 MLI.10: 7 residues within 4Å: Chain B: I.233, G.235, T.236, G.237, G.429, S.430 Ligands: MLI.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.236, B:T.236, B:T.236, B:T.236, B:G.237, B:S.430, B:S.430 Salt bridges: B:K.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weisse, R.H. et al., Structural basis of hexose specificity and catalytic properties of Kluyveromyces lactis glucokinase KlGlk1. To Be Published

Release Date

2025-05-14

Peptides

Glucokinase-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glucokinase-1

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