SMTL ID : 5od2.1 (2 other biounits)

Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

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

GLC.1: 15 residues within 4Å: Chain A: N.23, D.25, E.79, G.103, G.104, Q.105, I.108, N.169, I.171, I.196, Q.232, V.435, G.436, D.439 Ligands: PO4.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.23, A:D.25, A:E.79, A:G.104, A:Q.105, A:N.169, A:Q.232 Water bridges: A:N.21, A:K.167, A:K.167, A:K.167, A:R.194

1 x 5ID: (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL(Non-covalent)

5ID.2: 15 residues within 4Å: Chain A: S.192, H.345, T.346, Y.349, A.376, A.380, S.425, R.426, Y.427, V.428, P.431, T.434, L.437, G.438, I.441 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.427, A:L.437 Hydrogen bonds: A:T.346, A:V.428, A:V.428 Water bridges: A:T.373 Halogen bonds: A:S.192

1 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: PO4.4 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 8 residues within 4Å: Chain A: R.194, V.435, G.436, L.437, G.438, D.439 Ligands: GLC.1, MG.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.436, A:G.438, A:D.439, A:D.439 Water bridges: A:Q.105, A:Q.105, A:R.194, A:H.345, A:D.439 Salt bridges: A:R.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tokarz, P. et al., Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii in complex with 5-iodotubercidin reveals phosphoryl transfer mechanism. Protein Sci. (2018)

Release Date

2018-01-31

Peptides

Bifunctional ADP-specific glucokinase/phosphofructokinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bifunctional ADP-specific glucokinase/phosphofructokinase

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