SMTL ID : 4b8s.1

Crystal Structure of Thermococcus litoralis ADP-dependent Glucokinase (GK)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

monomer

Ligands

1 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 13 residues within 4Å: Chain A: N.38, N.40, D.42, E.96, G.119, G.120, Q.121, I.124, H.184, I.186, N.209, V.447, D.451 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.38, A:N.40, A:D.42, A:E.96, A:G.120, A:H.184, A:N.209, A:G.448 Water bridges: A:E.96, A:E.96, A:Q.121, A:G.448, A:D.451

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: E.279, A.281, G.303, L.304, N.305, E.308, H.352, G.450 Ligands: AMP.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.303, A:N.305 Water bridges: A:Q.121, A:Y.282, A:E.308, A:E.308, A:E.308, A:D.451 GOL.3: 8 residues within 4Å: Chain A: K.275, T.300, R.348, Y.363, F.458, E.461, F.462, R.465 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.363, A:E.461, A:E.461, A:E.461, A:R.465 Water bridges: A:R.465 GOL.4: 5 residues within 4Å: Chain A: N.22, A.26, E.367, D.370, M.464 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.22, A:D.370, A:D.370, A:M.464 Water bridges: A:N.25 GOL.5: 6 residues within 4Å: Chain A: P.142, Y.213, Y.218, M.219, R.220, R.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.218, A:R.220, A:R.224 GOL.7: 4 residues within 4Å: Chain A: D.318, E.319, E.320, L.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.320, A:L.321

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 15 residues within 4Å: Chain A: E.203, N.305, H.352, T.353, Y.354, Y.357, A.383, K.438, I.439, V.440, P.443, I.449, G.450, I.453 Ligands: GOL.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.203, A:N.305, A:H.352, A:T.353, A:V.440, A:V.440 Water bridges: A:Y.357, A:G.450, A:G.450 Salt bridges: A:H.352 pi-Stacking: A:Y.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rivas-Pardo, J.A. et al., Crystal Structure, Saxs and Kinetic Mechanism of Hyperthermophilic Adp-Dependent Glucokinase from Thermococcus Litoralis Reveal a Conserved Mechanism for Catalysis. Plos One (2013)

Release Date

2013-07-10

Peptides

ADP-DEPENDENT GLUCOKINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ADP-DEPENDENT GLUCOKINASE

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