SMTL ID : 9gro.2 (1 other biounit)

Crystal structure of the engineered C-terminal phosphatase domain from Saccharomyces cerevisiae Vip1 in complex with 1,5-InsP8 (phosphatase dead mutant, loop deletion residues 848-918)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.118, E.263, H.303, H.464 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.118, A:E.263, A:H.303, A:H.464

2 x 1JW: (2S)-hexane-1,2,6-triol(Non-covalent)

1JW.2: 7 residues within 4Å: Chain A: Q.459, L.460, D.461, R.463, Y.465, I.466, S.467 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.465 Hydrogen bonds: A:Y.465 1JW.4: 14 residues within 4Å: Chain A: Q.256, R.258, W.259, E.263, A.301, L.302, H.303, N.304, R.305, Q.306, F.307, L.460, H.464 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.263, A:Q.306, A:F.307, A:H.464

2 x PUT: 1,4-DIAMINOBUTANE(Non-covalent)

PUT.3: 5 residues within 4Å: Chain A: R.132, F.168, G.169, A.170, D.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.132, A:R.132 PUT.8: 11 residues within 4Å: Chain A: F.6, L.9, M.131, D.134, F.135, L.138, E.427, Y.429, K.445, K.471 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.6 Hydrogen bonds: A:D.134, A:Y.429

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

EDO.5: 4 residues within 4Å: Chain A: K.121, Y.122, T.125, Y.162 No protein-ligand interaction detected (PLIP) EDO.6: 12 residues within 4Å: Chain A: V.252, M.255, Q.256, R.258, W.259, E.263, D.264, P.265, F.268, N.304, F.307 Ligands: 1JW.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.304 EDO.7: 8 residues within 4Å: Chain A: Y.294, K.298, F.339, E.391, E.417, L.418, D.419, Y.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.298, A:L.418 EDO.9: 4 residues within 4Å: Chain A: P.407, L.478, D.479, Y.482 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.479 EDO.11: 7 residues within 4Å: Chain A: R.305, L.308, E.309, F.325, L.328, R.329, L.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.309 EDO.12: 9 residues within 4Å: Chain A: L.9, I.11, L.127, M.131, Q.423, T.425, E.427, K.471 Ligands: PUT.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.471

1 x I8P: (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)](Non-covalent)

I8P.10: 19 residues within 4Å: Chain A: K.21, K.23, K.25, E.43, K.90, Q.92, K.94, Q.107, I.109, K.111, E.153, R.155, D.187, N.189, K.192, K.199, S.288, K.390, S.392 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:Q.92, A:Q.92, A:S.288 Salt bridges: A:K.21, A:K.21, A:K.23, A:K.23, A:K.23, A:K.25, A:K.90, A:K.94, A:K.111, A:K.111, A:K.111, A:K.192, A:K.192, A:K.199, A:K.199, A:K.390, A:K.390

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raia, P. et al., A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis. Nat Commun (2025)

Release Date

2025-02-26

Peptides

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

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