SMTL ID : 6ilt.1

Structure of Arabidopsis thaliana Ribokinase complexed with ATP and Magnesium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: K.41, N.189, K.225, L.226, G.227, S.228, G.230, S.231, I.245, I.246, T.254, G.256, A.257, G.258, F.261, A.286 Ligands: MG.2, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.189, A:K.225, A:G.227, A:G.256, A:A.257, A:G.258 Water bridges: A:K.225, A:G.230, A:S.244, A:D.259, A:S.287, A:S.287 Salt bridges: A:K.41 ATP.5: 16 residues within 4Å: Chain B: N.189, K.225, L.226, G.227, G.230, I.245, I.246, V.251, T.254, G.256, A.257, G.258, F.261, A.286 Ligands: MG.6, MG.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.189, B:G.227, B:G.256, B:A.257, B:G.258 Water bridges: B:K.225, B:G.230, B:A.248 Salt bridges: B:K.41

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: K.41, E.192 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: K.41, D.167 Ligands: ATP.5 No protein-ligand interaction detected (PLIP)

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: D.253, T.255, C.289, V.292, G.294, S.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.289, A:S.298 NA.8: 6 residues within 4Å: Chain B: D.253, T.255, C.289, V.292, G.294, S.298 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.253, B:S.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kang, P.A. et al., Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana. J. Struct. Biol. (2019)

Release Date

2019-03-13

Peptides

Ribokinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ribokinase

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