SMTL ID : 4xf6.1 (1 other biounit)

myo-inositol 3-kinase bound with its products (ADP and 1D-myo-inositol 3-phosphate)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

monomer

Ligands

1 x LIP: L-MYO-INOSITOL-1-PHOSPHATE(Non-covalent)

LIP.1: 21 residues within 4Å: Chain A: V.10, D.12, G.25, G.26, G.27, Y.30, Y.75, R.85, L.87, V.112, Q.136, R.140, S.214, T.215, G.216, A.217, G.218, D.219 Ligands: ADP.2, INS.3, MG.4 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:D.12, A:G.26, A:R.85, A:Q.136, A:Q.136, A:R.140, A:R.140, A:G.216, A:G.216, A:A.217, A:G.218, A:D.219, A:D.219 Water bridges: A:Q.136 Salt bridges: A:R.85

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.2: 17 residues within 4Å: Chain A: N.83, H.164, D.166, S.187, N.188, G.189, P.190, F.204, P.206, V.207, V.209, A.217, G.218, T.245, L.249 Ligands: LIP.1, MG.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.83, A:N.83, A:S.187, A:S.187, A:G.189, A:G.218 Water bridges: A:R.85, A:D.166, A:D.166, A:N.188, A:V.207, A:V.209 Salt bridges: A:R.85, A:H.164

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

INS.3: 16 residues within 4Å: Chain A: D.12, G.25, G.26, G.27, Y.30, Y.75, L.77, R.85, L.87, V.112, Q.136, R.140, T.215, G.216, D.219 Ligands: LIP.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.26, A:G.26, A:R.85, A:Q.136, A:Q.136, A:R.140, A:R.140, A:G.216

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: Q.136, E.169 Ligands: LIP.1, ADP.2 No protein-ligand interaction detected (PLIP)

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

IOD.5: 2 residues within 4Å: Chain A: D.101 Ligands: IOD.10 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: T.203, E.269 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: E.91, R.92 Ligands: IOD.14 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: R.11, P.51 Ligand excluded by PLIP IOD.9: 1 residues within 4Å: Chain A: Q.236 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: P.100 Ligands: IOD.5 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: K.63 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: L.99 Ligand excluded by PLIP IOD.13: 2 residues within 4Å: Chain A: H.198, R.200 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: E.91, P.144 Ligands: IOD.7 Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: D.182, Y.229 Ligand excluded by PLIP

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.16: 2 residues within 4Å: Chain A: L.80, R.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.86, A:R.86

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
A

Carbohydrate/pyrimidine kinase, PfkB family

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