SMTL ID : 9gro.1 (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 SPM: SPERMINE(Non-covalent)

SPM.2: 11 residues within 4Å: Chain A: H.40, E.43, V.44, V.45, Q.92, D.187, S.188, N.189 Ligands: ORN.4, EDO.8, EDO.17 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.43, A:V.45 Hydrogen bonds: A:E.43, A:E.43, A:V.45, A:V.45 SPM.3: 14 residues within 4Å: Chain A: A.217, K.336, D.340, F.341, P.344, K.345, K.354, R.412, N.413, L.415, P.416, E.417, H.451, Q.453 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.340, A:F.341, A:R.412 Hydrogen bonds: A:K.336, A:D.340, A:K.354, A:E.417, A:H.451

1 x ORN: L-ornithine(Non-covalent)

ORN.4: 5 residues within 4Å: Chain A: D.187, S.188, N.189, A.190 Ligands: SPM.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.189, A:N.189

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

PUT.5: 8 residues within 4Å: Chain A: I.32, S.35, L.36, K.38, I.54, A.58, I.61 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) PUT.6: 12 residues within 4Å: Chain A: A.14, K.21, D.295, K.298, F.339, E.391, I.394, Y.395, L.418, D.419, Y.420, S.422 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:E.391 Hydrogen bonds: A:D.295, A:K.298, A:D.419, A:S.422 PUT.12: 8 residues within 4Å: Chain A: L.157, Q.161, L.173, G.174, S.175, E.177, I.178, I.180 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.178 Hydrogen bonds: A:G.174, A:I.178 PUT.18: 10 residues within 4Å: Chain A: N.145, I.146, K.147, D.372, D.375, M.376, R.379, A.383, C.384, V.385 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.383, A:V.385 Hydrogen bonds: A:D.372

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

EDO.7: 7 residues within 4Å: Chain A: L.36, K.38, I.46, D.51, I.54, V.55 Ligands: PUT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.36, A:D.51 EDO.8: 5 residues within 4Å: Chain A: V.45, R.47, K.182 Ligands: SPM.2, EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.47, A:R.47 EDO.9: 7 residues within 4Å: Chain A: L.56, R.60, L.63, K.74, A.77, N.78, E.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.60, A:N.78, A:E.81 EDO.10: 1 residues within 4Å: Chain A: K.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.53 EDO.11: 9 residues within 4Å: Chain A: Q.22, F.24, A.79, K.82, K.83, W.112, E.270, R.271, K.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.270 EDO.13: 5 residues within 4Å: Chain A: P.116, R.154, L.157, H.158, Q.161 No protein-ligand interaction detected (PLIP) EDO.14: 6 residues within 4Å: Chain A: Q.459, L.460, D.461, R.463, H.464, Y.465 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.461, A:D.461, A:H.464, A:Y.465 EDO.16: 7 residues within 4Å: Chain A: H.118, R.258, W.259, C.260, E.263, D.462, H.464 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.258, A:R.258, A:D.462 Water bridges: A:D.462 EDO.17: 7 residues within 4Å: Chain A: V.45, I.46, R.47, N.48, D.51 Ligands: SPM.2, EDO.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.47, A:N.48, A:D.51, A:D.51

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

I8P.15: 11 residues within 4Å: Chain A: K.25, H.26, S.27, K.72, K.105, Q.107, K.199, K.200, K.203, R.207, K.284 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.27, A:S.27 Salt bridges: A:K.25, A:K.25, A:K.25, A:H.26, A:K.72, A:K.72, A:K.72, A:K.105, A:K.199, A:K.200, A:K.203, A:K.203, A:K.203, A:R.207, A:K.284

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
A

Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase

Related Entries With Identical Sequence