SMTL ID : 8ppj.1 (1 other biounit)

Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate/ADP/Mn after reaction

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

ADP.1: 17 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: 661.2, MN.7, MN.8, MN.9 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.15, A:Q.67, A:L.69, A:D.80, A:D.80, A:K.154, A:K.154, A:D.234 Water bridges: A:D.234 Salt bridges: A:K.27, A:K.27

1 x 661: beta-D-glucopyranosylmethanol 3,4,6,1'-tetrakisphosphate(Non-covalent)

661.2: 13 residues within 4Å: Chain A: K.82, R.103, M.106, K.109, K.130, Y.133, R.137, E.151, D.234, K.237 Ligands: ADP.1, MN.7, MN.8 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:Y.133, A:Y.133 Water bridges: A:K.82, A:K.82, A:K.82, A:K.109, A:K.130, A:R.137, A:R.137, A:K.237, A:K.237 Salt bridges: A:K.82, A:R.103, A:K.109, A:K.130, A:K.130, A:R.137, A:K.165, A:K.237

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

SO4.3: 3 residues within 4Å: Chain A: R.170, S.275, R.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.275 Water bridges: A:S.275, A:R.279 Salt bridges: A:R.170, A:R.279 SO4.4: 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 SO4.5: 4 residues within 4Å: Chain A: S.169, E.171, Q.172, R.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.169, A:Q.172 Water bridges: A:E.171 Salt bridges: A:R.175 SO4.6: 6 residues within 4Å: Chain A: A.19, G.20, T.21, V.56, R.58, Q.65 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.20, A:T.21, A:T.21, A:Q.65 Salt bridges: A:R.58

3 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.7: 3 residues within 4Å: Chain A: D.234 Ligands: ADP.1, 661.2 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.234, H2O.2, H2O.4 MN.8: 2 residues within 4Å: Ligands: ADP.1, 661.2 No protein-ligand interaction detected (PLIP) MN.9: 2 residues within 4Å: Chain A: D.234 Ligands: ADP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.234, A:D.234, H2O.4, H2O.5

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
A

Inositol-trisphosphate 3-kinase A

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