SMTL ID : 4b8r.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: P.136, Y.158, L.169, N.233 Ligand excluded by PLIP GOL.2: 5 residues within 4Å: Chain A: K.45, Y.46, D.51, W.111, D.114 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: A.281, Y.282, N.305, V.307, E.308 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: M.341, D.342, G.345, Q.362, D.429, R.430 Ligands: GOL.8 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: Y.354, Y.356, N.403, R.405, A.406, L.409 Ligands: SO4.31 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: A.379, A.380, A.383, K.438, I.439, V.440, I.449 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: E.102, R.105, R.106, R.109 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: P.297, D.342, E.343, T.344, G.345 Ligands: GOL.4 Ligand excluded by PLIP GOL.9: 8 residues within 4Å: Chain A: N.144, V.159, P.160, V.161, A.175, R.220, E.222 Ligands: SO4.33 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: P.71, R.87, K.93, M.95, W.97 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: D.260, R.261, S.264 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: F.162, E.163, G.164, R.221 Ligands: SO4.33 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: E.100, S.101, E.102, E.103 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: T.446, V.447, G.448, I.449, G.450 Ligand excluded by PLIP GOL.15: 3 residues within 4Å: Chain A: S.264, N.267, R.271 Ligand excluded by PLIP

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

TRS.16: 6 residues within 4Å: Chain A: Y.282, R.286, R.289, S.311, E.314 Ligands: PEG.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.282, A:R.289, A:R.289, A:S.311 TRS.17: 11 residues within 4Å: Chain A: Q.121, E.279, A.281, G.303, L.304, N.305, E.308, H.352, G.450, D.451, S.454 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.121, A:E.279, A:G.303, A:E.308

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.18: 9 residues within 4Å: Chain A: N.40, D.42, E.96, G.119, G.120, I.124, H.184, I.207, V.447 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.40, A:N.40, A:D.42, A:G.120, A:H.184 Water bridges: A:Q.121 DTT.19: 5 residues within 4Å: Chain A: L.11, R.14, R.369, E.421, N.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.369, A:R.369, A:E.421, A:N.422

5 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.20: 7 residues within 4Å: Chain A: Y.282, V.307, A.310, S.311, E.314, L.326 Ligands: TRS.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.314 PEG.21: 4 residues within 4Å: Chain A: K.2, R.8, V.408, E.411 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.2, A:R.8, A:R.8 Water bridges: A:K.415 PEG.22: 6 residues within 4Å: Chain A: R.117, I.118, N.127, E.150, L.151, F.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.118, A:N.127, A:F.152 Water bridges: A:D.154, A:N.387 PEG.23: 4 residues within 4Å: Chain A: K.246, E.247, Y.248, N.285 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.247, A:Y.248, A:Y.248, A:N.285 Water bridges: A:A.284 PEG.24: 2 residues within 4Å: Chain A: R.271, Y.272 No protein-ligand interaction detected (PLIP)

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.25: 8 residues within 4Å: Chain A: T.300, E.347, Y.363, F.458, E.461, F.462, R.465 Ligands: SO4.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.465, A:R.465 PGE.26: 10 residues within 4Å: Chain A: L.269, N.270, N.273, V.274, K.275, P.297, K.298, F.299, T.300, E.347 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.274, A:K.275, A:P.297 Water bridges: A:S.276 PGE.27: 2 residues within 4Å: Chain A: R.224, R.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.224, A:R.261, A:R.261

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

SO4.28: 3 residues within 4Å: Chain A: N.273, K.275 Ligands: PGE.25 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.273 Water bridges: A:K.275, A:R.465, A:R.465 Salt bridges: A:K.275 SO4.29: 4 residues within 4Å: Chain A: K.385, R.390, Q.393, D.396 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.390, A:Q.393, A:D.396 Salt bridges: A:K.385 SO4.30: 7 residues within 4Å: Chain A: R.117, E.188, R.205, K.444, S.445, T.446, V.447 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.446, A:V.447, A:V.447 Salt bridges: A:R.117, A:R.205 SO4.31: 2 residues within 4Å: Chain A: R.405 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.405, A:R.405 Salt bridges: A:R.405 SO4.32: 1 residues within 4Å: Chain A: R.134 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.134 SO4.33: 6 residues within 4Å: Chain A: E.179, R.220, R.221, E.222 Ligands: GOL.9, GOL.12 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.220, A:R.220, A:R.221, A:R.221 Salt bridges: A:R.220, A:R.221

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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