SMTL ID : 8ppc.2 (1 other biounit)

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with L-chiro-inositol 2,3,5-trisphosphate/ATP/Mn

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x 2KM: L-chiro-inositol 2,3,5-trisphosphate(Non-covalent)

2KM.1: 11 residues within 4Å: Chain A: K.82, R.103, M.106, K.109, K.130, Y.133, M.134, R.137, K.237 Ligands: ATP.2, MN.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.82, A:K.109 Water bridges: A:K.82, A:K.82, A:R.103, A:K.130, A:R.137, A:R.149, A:R.149, A:R.149, A:K.237 Salt bridges: A:R.103, A:K.109, A:K.130, A:K.130, A:R.137, A:K.237

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

ATP.2: 15 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: 2KM.1, MN.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.15, A:Q.67, A:L.69, A:D.80, A:K.154, A:K.154, A:D.234 Water bridges: A:S.217 Salt bridges: A:K.27, A:K.27

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: D.234 Ligands: 2KM.1, ATP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.234, H2O.1

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

SO4.4: 1 residues within 4Å: Chain A: R.168 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.168 SO4.5: 2 residues within 4Å: Chain A: Q.172, R.175 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.172 Salt bridges: A:R.175 SO4.6: 3 residues within 4Å: Chain A: S.169, R.170, E.171 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.170, A:E.171 Water bridges: A:T.145, A:T.145, A:S.169, A:S.169

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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