SMTL ID : 8ppa.2 (2 other biounits)

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with D-myo-inositol 1,4,6-trisphosphate/AMP-PNP/Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

1 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 14 residues within 4Å: Chain A: H.3, S.15, F.16, K.27, P.50, Q.67, D.68, L.69, D.80, K.154, L.219, I.233, D.234 Ligands: 06G.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.15, A:K.27, A:Q.67, A:L.69, A:D.80, A:K.154, A:K.154, A:D.234 Water bridges: A:S.15, A:K.82, A:K.82, A:D.234, A:D.234 Salt bridges: A:K.27

1 x 06G: D-myo-inositol 1,4,6-trisphosphate(Non-covalent)

06G.2: 9 residues within 4Å: Chain A: K.82, R.103, M.106, K.109, K.130, Y.133, R.137, K.237 Ligands: ANP.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.109, A:K.109, A:R.137 Water bridges: A:K.82, A:K.82, A:K.82, A:K.130 Salt bridges: A:K.82, A:R.103, A:K.109, A:K.130, A:K.130, A:R.137, A:K.237

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

SO4.3: 3 residues within 4Å: Chain A: R.170, S.275, R.279 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.170, A:S.275 Water bridges: A:S.275 Salt bridges: A:R.279 SO4.4: 2 residues within 4Å: Chain A: S.169, R.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170, A:E.171 SO4.5: 2 residues within 4Å: Chain A: Q.172, R.175 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.172 Water bridges: A:R.175 Salt bridges: A:R.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marquez-Monino, M.A. et al., Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity. Nat Commun (2024)

Release Date

2024-02-28

Peptides

Inositol-trisphosphate 3-kinase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Inositol-trisphosphate 3-kinase A

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