SMTL ID : 4xf7.2 (1 other biounit)

myo-inositol 3-kinase bound with its substrates (AMPPCP and myo-inositol)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x INS: 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE(Non-covalent)

INS.1: 11 residues within 4Å: Chain A: V.10, D.12, G.25, G.26, G.27, Y.30, Y.75, V.112, Q.136, R.140, D.219 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.12, A:G.26, A:G.26, A:Q.136, A:Q.136, A:R.140, A:R.140 Water bridges: A:R.85, A:R.85, A:G.216

1 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.2: 20 residues within 4Å: Chain A: R.85, H.164, D.166, S.187, N.188, G.189, P.190, F.204, P.206, V.207, V.209, S.214, G.216, A.217, G.218, F.221, A.242, T.245, L.249 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.85, A:D.166, A:D.166, A:S.187, A:G.189, A:V.209, A:V.209, A:S.214, A:S.214, A:G.216, A:G.218 Water bridges: A:R.85, A:H.164, A:H.164, A:N.188

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: Q.136 Ligands: ACP.2 No protein-ligand interaction detected (PLIP)

10 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 3 residues within 4Å: Chain A: T.203, E.205, E.269 Ligand excluded by PLIP IOD.5: 2 residues within 4Å: Chain A: R.11, P.51 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: S.123, A.124 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: E.91, P.144 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: F.228, Q.231 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: Y.170 Ligands: IOD.13 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: K.239 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: Q.236 Ligand excluded by PLIP IOD.12: 4 residues within 4Å: Chain A: K.161, D.182, H.198, Y.229 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: S.177 Ligands: IOD.9 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagata, R. et al., Crystal Structure and Product Analysis of an Archaeal myo-Inositol Kinase Reveal Substrate Recognition Mode and 3-OH Phosphorylation. Biochemistry (2015)

Release Date

2015-06-03

Peptides

Carbohydrate/pyrimidine kinase, PfkB family: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Carbohydrate/pyrimidine kinase, PfkB family

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